This module generates a series of high level plots that describe the data overall and may be useful for identifying anomalous data and/or covariates.

Gene sets:

- Summary
- Chemokine receptors bind chemokines
- Costimulation by the CD28 family
- DAP12 interactions
- DAP12 signaling
- Degradation of the extracellular matrix
- Downstream signal transduction
- FCERI mediated MAPK activation
- G alpha (i) signalling events
- G alpha (q) signalling events
- G beta.CL.gamma signalling through PI3Kgamma
- Generic Transcription Pathway
- GPVI-mediated activation cascade
- Immunoregulatory interactions between a Lymphoid and a non-Lymph...
- Interleukin-1 signaling
- Metabolism of carbohydrates
- MicroRNA (miRNA) biogenesis
- MyD88.CL.Mal cascade initiated on plasma membrane
- Peptide ligand-binding receptors
- RAF-independent MAPK13 activation
- RAFMAP kinase cascade
- Role of LAT2NTALLAB on calcium mobilization
- Senescence-Associated Secretory Phenotype (SASP)
- Signaling by PDGF
- Signaling by SCF-KIT
- Signalling to p38 via RIT and RIN
- TNFR2 non-canonical NF-kB pathway
- TNFs bind their physiological receptors
- Transcriptional regulation of white adipocyte differentiation
- VEGFA-VEGFR2 Pathway
- VEGFR2 mediated cell proliferation

- Heatmaps
- PCA
- Study design
- Other QC

- Heatmaps

- Gender_1

- Covariates

- Other QC

- Heatmap of Raw Data
  More Plot Information Download detected/undetected calls data

  ##### Heatmap of Raw Data

  Heatmap of the raw counts. The plot is meant to provide an overview of how robust the raw expression levels are across samples and gene sets. Datasets that entirely lack higher level expressions (e.g. counts > 100) may indicate experimental failure or low input. The detected/undetected calls links to a .csv file stating whether each probe is above background, with 0/1 indicating below/above background. If the user has not specified a detection threshold, probes are called detected if they have more than double the counts of the median negative control.

- Heatmap of All Data
  More Plot Information

  ##### Heatmap of All Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of All Data
  More Plot Information

  ##### Principal Components of All Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- More Plot Information

  #####

  Pairwise comparisons of all covariates in the analysis. The type of plot is dependent on the types of variables compared; A categorical vs. categorical covariate plot is shown as a bar chart of counts (Y axis). Continuous vs. categorical covariates generate a boxplot with whiskers denoting 1.5 IQR. Continuous vs. continuous covariates are compared via a scatter plot. Variables that are correlated with a biological variable of interest are potential confounders that may influence downstream analyses. Additionally, bar plots and histograms show the distributions of categorical and continuous variables, respectively.

- Variance vs. Mean normalized signal plot across all targets/probes
  More Plot Information Mean and Variance statistics across all genes

  ##### Variance vs. Mean normalized signal plot across all targets/probes

  Each gene's variance in the log-scaled, normalized data is plotted against its mean value across all samples. Highly variable genes are indicated by gene name. Housekeeping genes are color coded according to their use in (or omission from) normalization.

- p-value distribution plots
  More Plot Information

  ##### p-value distribution plots

  For each covariate included in the analysis, a histogram of p-values testing each gene's univariate association with the chosen covariate is displayed. Covariates with largely flat histograms have minimal association with gene expression; covariates with histograms with significantly more mass on the left are either associated with the expression of many genes or are confounded with a covariate that is associated with the expression. Low p-values indicate strong evidence for an association.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Chemokine receptors bind chemokines Data
  More Plot Information

  ##### Heatmap of Chemokine receptors bind chemokines Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Chemokine receptors bind chemokines Data
  More Plot Information

  ##### Principal Components of Chemokine receptors bind chemokines Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Costimulation by the CD28 family Data
  More Plot Information

  ##### Heatmap of Costimulation by the CD28 family Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Costimulation by the CD28 family Data
  More Plot Information

  ##### Principal Components of Costimulation by the CD28 family Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of DAP12 interactions Data
  More Plot Information

  ##### Heatmap of DAP12 interactions Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of DAP12 interactions Data
  More Plot Information

  ##### Principal Components of DAP12 interactions Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of DAP12 signaling Data
  More Plot Information

  ##### Heatmap of DAP12 signaling Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of DAP12 signaling Data
  More Plot Information

  ##### Principal Components of DAP12 signaling Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Degradation of the extracellular matrix Data
  More Plot Information

  ##### Heatmap of Degradation of the extracellular matrix Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Degradation of the extracellular matrix Data
  More Plot Information

  ##### Principal Components of Degradation of the extracellular matrix Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Downstream signal transduction Data
  More Plot Information

  ##### Heatmap of Downstream signal transduction Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Downstream signal transduction Data
  More Plot Information

  ##### Principal Components of Downstream signal transduction Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of FCERI mediated MAPK activation Data
  More Plot Information

  ##### Heatmap of FCERI mediated MAPK activation Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of FCERI mediated MAPK activation Data
  More Plot Information

  ##### Principal Components of FCERI mediated MAPK activation Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of G alpha (i) signalling events Data
  More Plot Information

  ##### Heatmap of G alpha (i) signalling events Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of G alpha (i) signalling events Data
  More Plot Information

  ##### Principal Components of G alpha (i) signalling events Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of G alpha (q) signalling events Data
  More Plot Information

  ##### Heatmap of G alpha (q) signalling events Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of G alpha (q) signalling events Data
  More Plot Information

  ##### Principal Components of G alpha (q) signalling events Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of G beta.CL.gamma signalling through PI3Kgamma Data
  More Plot Information

  ##### Heatmap of G beta.CL.gamma signalling through PI3Kgamma Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of G beta.CL.gamma signalling through PI3Kgamma Data
  More Plot Information

  ##### Principal Components of G beta.CL.gamma signalling through PI3Kgamma Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Generic Transcription Pathway Data
  More Plot Information

  ##### Heatmap of Generic Transcription Pathway Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Generic Transcription Pathway Data
  More Plot Information

  ##### Principal Components of Generic Transcription Pathway Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of GPVI-mediated activation cascade Data
  More Plot Information

  ##### Heatmap of GPVI-mediated activation cascade Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of GPVI-mediated activation cascade Data
  More Plot Information

  ##### Principal Components of GPVI-mediated activation cascade Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Data
  More Plot Information

  ##### Heatmap of Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Data
  More Plot Information

  ##### Principal Components of Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Interleukin-1 signaling Data
  More Plot Information

  ##### Heatmap of Interleukin-1 signaling Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Interleukin-1 signaling Data
  More Plot Information

  ##### Principal Components of Interleukin-1 signaling Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Metabolism of carbohydrates Data
  More Plot Information

  ##### Heatmap of Metabolism of carbohydrates Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Metabolism of carbohydrates Data
  More Plot Information

  ##### Principal Components of Metabolism of carbohydrates Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of MyD88.CL.Mal cascade initiated on plasma membrane Data
  More Plot Information

  ##### Heatmap of MyD88.CL.Mal cascade initiated on plasma membrane Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of MyD88.CL.Mal cascade initiated on plasma membrane Data
  More Plot Information

  ##### Principal Components of MyD88.CL.Mal cascade initiated on plasma membrane Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Peptide ligand-binding receptors Data
  More Plot Information

  ##### Heatmap of Peptide ligand-binding receptors Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Peptide ligand-binding receptors Data
  More Plot Information

  ##### Principal Components of Peptide ligand-binding receptors Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of RAF-independent MAPK13 activation Data
  More Plot Information

  ##### Heatmap of RAF-independent MAPK13 activation Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of RAF-independent MAPK13 activation Data
  More Plot Information

  ##### Principal Components of RAF-independent MAPK13 activation Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of RAFMAP kinase cascade Data
  More Plot Information

  ##### Heatmap of RAFMAP kinase cascade Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of RAFMAP kinase cascade Data
  More Plot Information

  ##### Principal Components of RAFMAP kinase cascade Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Role of LAT2NTALLAB on calcium mobilization Data
  More Plot Information

  ##### Heatmap of Role of LAT2NTALLAB on calcium mobilization Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Role of LAT2NTALLAB on calcium mobilization Data
  More Plot Information

  ##### Principal Components of Role of LAT2NTALLAB on calcium mobilization Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Senescence-Associated Secretory Phenotype (SASP) Data
  More Plot Information

  ##### Heatmap of Senescence-Associated Secretory Phenotype (SASP) Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Senescence-Associated Secretory Phenotype (SASP) Data
  More Plot Information

  ##### Principal Components of Senescence-Associated Secretory Phenotype (SASP) Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Signaling by PDGF Data
  More Plot Information

  ##### Heatmap of Signaling by PDGF Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Signaling by PDGF Data
  More Plot Information

  ##### Principal Components of Signaling by PDGF Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Signaling by SCF-KIT Data
  More Plot Information

  ##### Heatmap of Signaling by SCF-KIT Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Signaling by SCF-KIT Data
  More Plot Information

  ##### Principal Components of Signaling by SCF-KIT Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Signalling to p38 via RIT and RIN Data
  More Plot Information

  ##### Heatmap of Signalling to p38 via RIT and RIN Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Signalling to p38 via RIT and RIN Data
  More Plot Information

  ##### Principal Components of Signalling to p38 via RIT and RIN Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of TNFR2 non-canonical NF-kB pathway Data
  More Plot Information

  ##### Heatmap of TNFR2 non-canonical NF-kB pathway Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of TNFR2 non-canonical NF-kB pathway Data
  More Plot Information

  ##### Principal Components of TNFR2 non-canonical NF-kB pathway Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of TNFs bind their physiological receptors Data
  More Plot Information

  ##### Heatmap of TNFs bind their physiological receptors Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of TNFs bind their physiological receptors Data
  More Plot Information

  ##### Principal Components of TNFs bind their physiological receptors Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of Transcriptional regulation of white adipocyte differentiation Data
  More Plot Information

  ##### Heatmap of Transcriptional regulation of white adipocyte differentiation Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of Transcriptional regulation of white adipocyte differentiation Data
  More Plot Information

  ##### Principal Components of Transcriptional regulation of white adipocyte differentiation Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of VEGFA-VEGFR2 Pathway Data
  More Plot Information

  ##### Heatmap of VEGFA-VEGFR2 Pathway Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of VEGFA-VEGFR2 Pathway Data
  More Plot Information

  ##### Principal Components of VEGFA-VEGFR2 Pathway Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

- Heatmaps
- PCA

- Heatmaps

- Gender_1

- Heatmap of VEGFR2 mediated cell proliferation Data
  More Plot Information

  ##### Heatmap of VEGFR2 mediated cell proliferation Data

  Heatmap of the normalized data, scaled to give all genes equal variance, generated via unsupervised clustering. Orange indicates high expression; blue indicates low expression. This plot is meant to provide a high level exploratory view of the data.

- Principal Components of VEGFR2 mediated cell proliferation Data
  More Plot Information

  ##### Principal Components of VEGFR2 mediated cell proliferation Data

  Principal component analysis maps high-dimensional datasets onto a smaller number of highly informative dimensions. Here, the first four principal components of the gene expression data are plotted against each other and colored by the values of the selected covariate. This plot may be used to identify clusters in the data and to identify variables associated with prominent signal in the data. Variables that are associated with these leading principal components should be considered in downstream analyses.

- Outliers
  More Plot Information

  | Outlier on PC 1 | Outlier on PC 2 | Outlier on PC 3 | Outlier on PC 4
  20180330_0064-004_0064-0007_04.RCC | TRUE | FALSE | FALSE | FALSE
  20180407_0064-009_0064-0120_12.RCC | FALSE | TRUE | FALSE | FALSE

  ##### Outliers

  Table identifying outliers in the first four PCs of the data.

Displays plots that detail the impact of normalization on the data.

Analyte:
- mRNA

- Pairwise Variance during HK Selection
  More Plot Information

  ##### Pairwise Variance during HK Selection

  Displays the geNorm pairwise variation statistic after successive genes are removed. This statistic cannot be computed for the final two genes, which are therefore not displayed. The ideal normalization gene set will minimize the pairwise variation statistic.

- Normalization Summary: mRNA
  More Plot Information mRNA Normalization Summary Data All Normalized Data mRNA Normalized Data Download HK Genes

  ##### Normalization Summary: mRNA

  The lower the MSE of reference profile the higher quality of normalization. The more positive normalization factor, the higher counts were registered for the sample and vice versa

Pathway scores condense each sample's gene expression profile into a small set of pathway scores. An experiment can then be explored through the lens of pathway scores instead of in the much higher-dimension lens of gene expression values. Pathway scores are fit using the first principal component of each gene set's data. They are oriented such that increasing score corresponds to mostly increasing expression (specifically, each pathway score has positive weights for at least half its genes). Summary plots explore the joint behavior of pathways, and Covariates plots compare pathway scores to covariates.

- Summary
- Covariates

- score

- score

Choose a Pathway:

- Summary
- Chemokine receptors bind chemokines
- Costimulation by the CD28 family
- DAP12 interactions
- DAP12 signaling
- Downstream signal transduction
- FCERI mediated MAPK activation
- G alpha (i) signalling events
- G alpha (q) signalling events
- Generic Transcription Pathway
- GPVI-mediated activation cascade
- Immunoregulatory interactions between a Lymphoid and a non-Lymph...
- Metabolism of carbohydrates
- MyD88.CL.Mal cascade initiated on plasma membrane
- Peptide ligand-binding receptors
- RAF-independent MAPK13 activation
- RAFMAP kinase cascade
- Signaling by PDGF
- Signaling by SCF-KIT
- Signalling to p38 via RIT and RIN
- TNFR2 non-canonical NF-kB pathway
- TNFs bind their physiological receptors
- VEGFA-VEGFR2 Pathway
- VEGFR2 mediated cell proliferation

- Heatmap of Pathway scores
  More Plot Information Download Pathway scores

  ##### Heatmap of Pathway scores

  Heatmap showing pathway score. This plot is a high level overview of how the pathway scores change across samples. Use it to understand how pathway scores cluster together and which samples exhibit similar pathway score profiles. Orange indicates high scores; blue indicates low scores. Scores are displayed on the same scale via a Z-transformation.

- Heatmap of Correlation Matrix of Pathway scores
  More Plot Information

  ##### Heatmap of Correlation Matrix of Pathway scores

  Heatmap showing the correlation matrix of pathway scores. Orange and blue indicate positive and negative correlation, respectively.

- Chemokine receptors bind chemokines measurements vs. other pathway scores
  More Plot Information

  ##### Chemokine receptors bind chemokines measurements vs. other pathway scores

  Each panel plots Chemokine receptors bind chemokines against another pathway score. Points are colored by Gender_1.

- Costimulation by the CD28 family measurements vs. other pathway scores
  More Plot Information

  ##### Costimulation by the CD28 family measurements vs. other pathway scores

  Each panel plots Costimulation by the CD28 family against another pathway score. Points are colored by Gender_1.

- DAP12 interactions measurements vs. other pathway scores
  More Plot Information

  ##### DAP12 interactions measurements vs. other pathway scores

  Each panel plots DAP12 interactions against another pathway score. Points are colored by Gender_1.

- DAP12 signaling measurements vs. other pathway scores
  More Plot Information

  ##### DAP12 signaling measurements vs. other pathway scores

  Each panel plots DAP12 signaling against another pathway score. Points are colored by Gender_1.

- Downstream signal transduction measurements vs. other pathway scores
  More Plot Information

  ##### Downstream signal transduction measurements vs. other pathway scores

  Each panel plots Downstream signal transduction against another pathway score. Points are colored by Gender_1.

- FCERI mediated MAPK activation measurements vs. other pathway scores
  More Plot Information

  ##### FCERI mediated MAPK activation measurements vs. other pathway scores

  Each panel plots FCERI mediated MAPK activation against another pathway score. Points are colored by Gender_1.

- G alpha (i) signalling events measurements vs. other pathway scores
  More Plot Information

  ##### G alpha (i) signalling events measurements vs. other pathway scores

  Each panel plots G alpha (i) signalling events against another pathway score. Points are colored by Gender_1.

- G alpha (q) signalling events measurements vs. other pathway scores
  More Plot Information

  ##### G alpha (q) signalling events measurements vs. other pathway scores

  Each panel plots G alpha (q) signalling events against another pathway score. Points are colored by Gender_1.

- Generic Transcription Pathway measurements vs. other pathway scores
  More Plot Information

  ##### Generic Transcription Pathway measurements vs. other pathway scores

  Each panel plots Generic Transcription Pathway against another pathway score. Points are colored by Gender_1.

- GPVI-mediated activation cascade measurements vs. other pathway scores
  More Plot Information

  ##### GPVI-mediated activation cascade measurements vs. other pathway scores

  Each panel plots GPVI-mediated activation cascade against another pathway score. Points are colored by Gender_1.

- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell measurements vs. other pathway scores
  More Plot Information

  ##### Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell measurements vs. other pathway scores

  Each panel plots Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell against another pathway score. Points are colored by Gender_1.

- Metabolism of carbohydrates measurements vs. other pathway scores
  More Plot Information

  ##### Metabolism of carbohydrates measurements vs. other pathway scores

  Each panel plots Metabolism of carbohydrates against another pathway score. Points are colored by Gender_1.

- MyD88.CL.Mal cascade initiated on plasma membrane measurements vs. other pathway scores
  More Plot Information

  ##### MyD88.CL.Mal cascade initiated on plasma membrane measurements vs. other pathway scores

  Each panel plots MyD88.CL.Mal cascade initiated on plasma membrane against another pathway score. Points are colored by Gender_1.

- Peptide ligand-binding receptors measurements vs. other pathway scores
  More Plot Information

  ##### Peptide ligand-binding receptors measurements vs. other pathway scores

  Each panel plots Peptide ligand-binding receptors against another pathway score. Points are colored by Gender_1.

- RAF-independent MAPK13 activation measurements vs. other pathway scores
  More Plot Information

  ##### RAF-independent MAPK13 activation measurements vs. other pathway scores

  Each panel plots RAF-independent MAPK13 activation against another pathway score. Points are colored by Gender_1.

- RAFMAP kinase cascade measurements vs. other pathway scores
  More Plot Information

  ##### RAFMAP kinase cascade measurements vs. other pathway scores

  Each panel plots RAFMAP kinase cascade against another pathway score. Points are colored by Gender_1.

- Signaling by PDGF measurements vs. other pathway scores
  More Plot Information

  ##### Signaling by PDGF measurements vs. other pathway scores

  Each panel plots Signaling by PDGF against another pathway score. Points are colored by Gender_1.

- Signaling by SCF-KIT measurements vs. other pathway scores
  More Plot Information

  ##### Signaling by SCF-KIT measurements vs. other pathway scores

  Each panel plots Signaling by SCF-KIT against another pathway score. Points are colored by Gender_1.

- Signalling to p38 via RIT and RIN measurements vs. other pathway scores
  More Plot Information

  ##### Signalling to p38 via RIT and RIN measurements vs. other pathway scores

  Each panel plots Signalling to p38 via RIT and RIN against another pathway score. Points are colored by Gender_1.

- TNFR2 non-canonical NF-kB pathway measurements vs. other pathway scores
  More Plot Information

  ##### TNFR2 non-canonical NF-kB pathway measurements vs. other pathway scores

  Each panel plots TNFR2 non-canonical NF-kB pathway against another pathway score. Points are colored by Gender_1.

- TNFs bind their physiological receptors measurements vs. other pathway scores
  More Plot Information

  ##### TNFs bind their physiological receptors measurements vs. other pathway scores

  Each panel plots TNFs bind their physiological receptors against another pathway score. Points are colored by Gender_1.

- VEGFA-VEGFR2 Pathway measurements vs. other pathway scores
  More Plot Information

  ##### VEGFA-VEGFR2 Pathway measurements vs. other pathway scores

  Each panel plots VEGFA-VEGFR2 Pathway against another pathway score. Points are colored by Gender_1.

- VEGFR2 mediated cell proliferation measurements vs. other pathway scores
  More Plot Information

  ##### VEGFR2 mediated cell proliferation measurements vs. other pathway scores

  Each panel plots VEGFR2 mediated cell proliferation against another pathway score. Points are colored by Gender_1.

Choose a Pathway:

- Summary
- Chemokine receptors bind chemokines
- Costimulation by the CD28 family
- DAP12 interactions
- DAP12 signaling
- Downstream signal transduction
- FCERI mediated MAPK activation
- G alpha (i) signalling events
- G alpha (q) signalling events
- Generic Transcription Pathway
- GPVI-mediated activation cascade
- Immunoregulatory interactions between a Lymphoid and a non-Lymph...
- Metabolism of carbohydrates
- MyD88.CL.Mal cascade initiated on plasma membrane
- Peptide ligand-binding receptors
- RAF-independent MAPK13 activation
- RAFMAP kinase cascade
- Signaling by PDGF
- Signaling by SCF-KIT
- Signalling to p38 via RIT and RIN
- TNFR2 non-canonical NF-kB pathway
- TNFs bind their physiological receptors
- VEGFA-VEGFR2 Pathway
- VEGFR2 mediated cell proliferation

- Pathway scores vs. Gender_1
  More Plot Information

  ##### Pathway scores vs. Gender_1

  Plots the pathway scores against Gender_1. The pathway scores are plotted to show how they vary across different values of Gender_1 conditions. Lines show each pathway's average score across values of Gender_1.

- Chemokine receptors bind chemokines pathway scores vs. Gender_1
  More Plot Information

  ##### Chemokine receptors bind chemokines pathway scores vs. Gender_1

  Plots Chemokine receptors bind chemokines pathway scores against Gender_1.

- Costimulation by the CD28 family pathway scores vs. Gender_1
  More Plot Information

  ##### Costimulation by the CD28 family pathway scores vs. Gender_1

  Plots Costimulation by the CD28 family pathway scores against Gender_1.

- DAP12 interactions pathway scores vs. Gender_1
  More Plot Information

  ##### DAP12 interactions pathway scores vs. Gender_1

  Plots DAP12 interactions pathway scores against Gender_1.

- DAP12 signaling pathway scores vs. Gender_1
  More Plot Information

  ##### DAP12 signaling pathway scores vs. Gender_1

  Plots DAP12 signaling pathway scores against Gender_1.

- Downstream signal transduction pathway scores vs. Gender_1
  More Plot Information

  ##### Downstream signal transduction pathway scores vs. Gender_1

  Plots Downstream signal transduction pathway scores against Gender_1.

- FCERI mediated MAPK activation pathway scores vs. Gender_1
  More Plot Information

  ##### FCERI mediated MAPK activation pathway scores vs. Gender_1

  Plots FCERI mediated MAPK activation pathway scores against Gender_1.

- G alpha (i) signalling events pathway scores vs. Gender_1
  More Plot Information

  ##### G alpha (i) signalling events pathway scores vs. Gender_1

  Plots G alpha (i) signalling events pathway scores against Gender_1.

- G alpha (q) signalling events pathway scores vs. Gender_1
  More Plot Information

  ##### G alpha (q) signalling events pathway scores vs. Gender_1

  Plots G alpha (q) signalling events pathway scores against Gender_1.

- Generic Transcription Pathway pathway scores vs. Gender_1
  More Plot Information

  ##### Generic Transcription Pathway pathway scores vs. Gender_1

  Plots Generic Transcription Pathway pathway scores against Gender_1.

- GPVI-mediated activation cascade pathway scores vs. Gender_1
  More Plot Information

  ##### GPVI-mediated activation cascade pathway scores vs. Gender_1

  Plots GPVI-mediated activation cascade pathway scores against Gender_1.

- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell pathway scores vs. Gender_1
  More Plot Information

  ##### Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell pathway scores vs. Gender_1

  Plots Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell pathway scores against Gender_1.

- Metabolism of carbohydrates pathway scores vs. Gender_1
  More Plot Information

  ##### Metabolism of carbohydrates pathway scores vs. Gender_1

  Plots Metabolism of carbohydrates pathway scores against Gender_1.

- MyD88.CL.Mal cascade initiated on plasma membrane pathway scores vs. Gender_1
  More Plot Information

  ##### MyD88.CL.Mal cascade initiated on plasma membrane pathway scores vs. Gender_1

  Plots MyD88.CL.Mal cascade initiated on plasma membrane pathway scores against Gender_1.

- Peptide ligand-binding receptors pathway scores vs. Gender_1
  More Plot Information

  ##### Peptide ligand-binding receptors pathway scores vs. Gender_1

  Plots Peptide ligand-binding receptors pathway scores against Gender_1.

- RAF-independent MAPK13 activation pathway scores vs. Gender_1
  More Plot Information

  ##### RAF-independent MAPK13 activation pathway scores vs. Gender_1

  Plots RAF-independent MAPK13 activation pathway scores against Gender_1.

- RAFMAP kinase cascade pathway scores vs. Gender_1
  More Plot Information

  ##### RAFMAP kinase cascade pathway scores vs. Gender_1

  Plots RAFMAP kinase cascade pathway scores against Gender_1.

- Signaling by PDGF pathway scores vs. Gender_1
  More Plot Information

  ##### Signaling by PDGF pathway scores vs. Gender_1

  Plots Signaling by PDGF pathway scores against Gender_1.

- Signaling by SCF-KIT pathway scores vs. Gender_1
  More Plot Information

  ##### Signaling by SCF-KIT pathway scores vs. Gender_1

  Plots Signaling by SCF-KIT pathway scores against Gender_1.

- Signalling to p38 via RIT and RIN pathway scores vs. Gender_1
  More Plot Information

  ##### Signalling to p38 via RIT and RIN pathway scores vs. Gender_1

  Plots Signalling to p38 via RIT and RIN pathway scores against Gender_1.

- TNFR2 non-canonical NF-kB pathway pathway scores vs. Gender_1
  More Plot Information

  ##### TNFR2 non-canonical NF-kB pathway pathway scores vs. Gender_1

  Plots TNFR2 non-canonical NF-kB pathway pathway scores against Gender_1.

- TNFs bind their physiological receptors pathway scores vs. Gender_1
  More Plot Information

  ##### TNFs bind their physiological receptors pathway scores vs. Gender_1

  Plots TNFs bind their physiological receptors pathway scores against Gender_1.

- VEGFA-VEGFR2 Pathway pathway scores vs. Gender_1
  More Plot Information

  ##### VEGFA-VEGFR2 Pathway pathway scores vs. Gender_1

  Plots VEGFA-VEGFR2 Pathway pathway scores against Gender_1.

- VEGFR2 mediated cell proliferation pathway scores vs. Gender_1
  More Plot Information

  ##### VEGFR2 mediated cell proliferation pathway scores vs. Gender_1

  Plots VEGFR2 mediated cell proliferation pathway scores against Gender_1.

Genes are tested for differential expression in response to each selected covariate. For each gene, a single linear regression is fit using all selected covariates to predict expression. This approach eliminates confounding due to measured covariates and isolates the independent association of each covariate with gene expression, measuring each variable's association with a gene after holding all other variables constant.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change with the selected covariate. Highly statistically significant genes fall at the top of the plot above the horizontal lines, and highly differentially expressed genes fall to either side. Horizontal lines indicate various False Discovery Rate (FDR) thresholds or p-value thresholds if there is no adjustment to the p-values. Genes are colored if the resulting p-value is below the given FDR or p-value threshold. The 40 most statistically significant genes are labeled in the plot.

- DE Results: Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | probe.ID
  MME-mRNA | 4.7 | 0.556 | 3.61 | 5.79 | 26 | 12.2 | 55.3 | 4.16e-13 | 5.62e-10 | Wald |  | NM_007288.2:258
  Il1rn-mRNA | 2.77 | 0.396 | 1.99 | 3.55 | 6.82 | 3.98 | 11.7 | 3.92e-10 | 2.64e-07 | lm.nb | Interleukin-1 signaling | NM_000577.3:480
  FPR2-mRNA | 1.79 | 0.308 | 1.19 | 2.4 | 3.47 | 2.28 | 5.27 | 8.3e-08 | 3.73e-05 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | NM_001462.3:1200
  CEBPB-mRNA | 1.09 | 0.256 | 0.59 | 1.6 | 2.13 | 1.51 | 3.02 | 4.82e-05 | 0.0163 | lm.nb | Senescence-Associated Secretory Phenotype (SASP), Transcriptional regulation of white adipocyte differentiation | NM_005194.2:1420
  BCL6-mRNA | 1.4 | 0.383 | 0.653 | 2.16 | 2.65 | 1.57 | 4.46 | 0.000412 | 0.111 | lm.nb |  | NM_138931.1:505
  CR2-mRNA | 1.22 | 0.36 | 0.511 | 1.92 | 2.33 | 1.43 | 3.8 | 0.00106 | 0.239 | lm.nb |  | NM_001006658.1:485
  TNFRSF4-mRNA | -1.12 | 0.346 | -1.8 | -0.444 | 0.46 | 0.287 | 0.735 | 0.00165 | 0.317 | Wald | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | NM_003327.3:981
  TNF-mRNA | 1.1 | 0.343 | 0.423 | 1.77 | 2.14 | 1.34 | 3.41 | 0.00192 | 0.324 | lm.nb |  | NM_000594.2:1010
  Ier3-mRNA | 0.973 | 0.32 | 0.345 | 1.6 | 1.96 | 1.27 | 3.03 | 0.0031 | 0.465 | lm.nb |  | NM_003897.3:527
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | NM_002183.2:745
  TNFRSF17-mRNA | 0.904 | 0.313 | 0.291 | 1.52 | 1.87 | 1.22 | 2.86 | 0.00478 | 0.587 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | NM_001192.2:635
  Ccl2-mRNA | -0.471 | 0.17 | -0.804 | -0.138 | 0.722 | 0.573 | 0.909 | 0.00677 | 0.738 | Wald | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | NM_002982.3:0
  NFATC4-mRNA | -1.42 | 0.521 | -2.44 | -0.401 | 0.373 | 0.184 | 0.757 | 0.00757 | 0.738 | Wald |  | NM_001136022.2:2296
  NLRP2-mRNA | 1 | 0.368 | 0.28 | 1.72 | 2 | 1.21 | 3.3 | 0.00777 | 0.738 | lm.nb |  | NM_017852.1:2870
  Cd300lb-mRNA | 0.721 | 0.271 | 0.19 | 1.25 | 1.65 | 1.14 | 2.38 | 0.00913 | 0.738 | lm.nb | DAP12 interactions, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | NM_174892.3:226
  CD19-mRNA | 1.09 | 0.409 | 0.286 | 1.89 | 2.12 | 1.22 | 3.7 | 0.00924 | 0.738 | lm.nb |  | XM_011545981.1:713
  Pfkfb3-mRNA | 0.978 | 0.369 | 0.255 | 1.7 | 1.97 | 1.19 | 3.25 | 0.00939 | 0.738 | lm.nb | Metabolism of carbohydrates | NM_004566.3:710
  MAPK13-mRNA | 0.881 | 0.334 | 0.226 | 1.54 | 1.84 | 1.17 | 2.9 | 0.00985 | 0.738 | lm.nb | VEGFA-VEGFR2 Pathway | NM_002754.3:1050
  HPSE-mRNA | 0.666 | 0.265 | 0.147 | 1.19 | 1.59 | 1.11 | 2.27 | 0.0137 | 0.963 | lm.nb | Metabolism of carbohydrates | NM_006665.3:1625
  SAAS-mRNA | 0.553 | 0.221 | 0.119 | 0.986 | 1.47 | 1.09 | 1.98 | 0.0143 | 0.963 | Wald |  | NM_013271.2:570

  ##### DE Results: Gender_1: 2 vs.1

  Table presenting the most statistically significantly differentially expressed genes with the selected covariate. 'Estimated log fold-change' estimates a gene's differential expression. For categorical covariates, a gene is estimated to have 2^(log fold change) times its expression in baseline samples, holding all other variables in the analysis constant. If the covariate is continuous, for each unit increase in the selected covariate, a gene's expression is estimated to increase by 2^(log fold change)-fold, holding all other variables in the analysis constant. The 95% confidence interval for the log fold change is also presented, along with a p-value and an adjusted p-value or FDR if requested. Method column indicates the model used to estimate differential expression. Mixed negative binomial model uses the mle function to run the Wald test. The simplified negative binomial model uses the glm.nb function . The loglinear model uses the lm function.

The results of differential expression testing are summarized at the gene set level. Each gene set's most differentially expressed genes are identified, and the extent of differential expression in each gene set is summarized using a 'global significance score'.

Gene sets:

- Summary
- Chemokine receptors bind chemokines
- Costimulation by the CD28 family
- DAP12 interactions
- DAP12 signaling
- Degradation of the extracellular matrix
- Downstream signal transduction
- FCERI mediated MAPK activation
- G alpha (i) signalling events
- G alpha (q) signalling events
- G beta.CL.gamma signalling through PI3Kgamma
- Generic Transcription Pathway
- GPVI-mediated activation cascade
- Immunoregulatory interactions between a Lymphoid and a non-Lymph...
- Interleukin-1 signaling
- Metabolism of carbohydrates
- MicroRNA (miRNA) biogenesis
- MyD88.CL.Mal cascade initiated on plasma membrane
- Peptide ligand-binding receptors
- RAF-independent MAPK13 activation
- RAFMAP kinase cascade
- Role of LAT2NTALLAB on calcium mobilization
- Senescence-Associated Secretory Phenotype (SASP)
- Signaling by PDGF
- Signaling by SCF-KIT
- Signalling to p38 via RIT and RIN
- TNFR2 non-canonical NF-kB pathway
- TNFs bind their physiological receptors
- Transcriptional regulation of white adipocyte differentiation
- VEGFA-VEGFR2 Pathway
- VEGFR2 mediated cell proliferation

- Undirected and Directed global significance scores table
  More Plot Information Download CSV Data

  | Undirected Gender_1: differential expression in 2 vs. baseline of 1 | Directed Gender_1: differential expression in 2 vs. baseline of 1
  Chemokine receptors bind chemokines | 1.5 | 0.918
  Costimulation by the CD28 family | 0.83 | 0.421
  DAP12 interactions | 1.401 | 1.227
  DAP12 signaling | 1.273 | 1.065
  Degradation of the extracellular matrix | 0.801 | -0.687
  Downstream signal transduction | 1.282 | 1.076
  FCERI mediated MAPK activation | 1.532 | 1.321
  G alpha (i) signalling events | 1.934 | 1.797
  G alpha (q) signalling events | 2.89 | 2.66
  G beta.CL.gamma signalling through PI3Kgamma | 1.851 | 1.609
  Generic Transcription Pathway | 0.587 | 0.545
  GPVI-mediated activation cascade | 1.656 | 1.439
  Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | 1.055 | 0.85
  Interleukin-1 signaling | 3.212 | 3.208
  Metabolism of carbohydrates | 1.548 | 1.514
  MicroRNA (miRNA) biogenesis | 0.493 | 0.364
  MyD88.CL.Mal cascade initiated on plasma membrane | 1.193 | 1.193
  Peptide ligand-binding receptors | 2.028 | 1.63
  RAF-independent MAPK13 activation | 1.371 | 1.371
  RAFMAP kinase cascade | 1.43 | 1.179

  ##### Undirected and Directed global significance scores table

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Chemokine receptors bind chemokines genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  Ccl2-mRNA | -0.471 | 0.17 | -0.804 | -0.138 | 0.722 | 0.573 | 0.909 | 0.00677 | 0.738 | Wald | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl2 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04621;hsa04668;hsa04933;hsa05142;hsa05144;hsa05164;hsa05168;hsa05323 |  | CCL2 | NA | azure4 | 1 | -2.77058823529412
  Ccl4-mRNA | 0.936 | 0.396 | 0.16 | 1.71 | 1.91 | 1.12 | 3.28 | 0.0202 | 1 | lm.nb | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl4 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04620;hsa04623;hsa05132 |  | CCL4 | NA | azure4 | 1 | 2.36363636363636
  Cxcl10-mRNA | 0.621 | 0.345 | -0.055 | 1.3 | 1.54 | 0.963 | 2.46 | 0.075 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Cxcl10 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04620;hsa04622;hsa04623;hsa04668;hsa05164 |  | CXCL10 | NA | azure4 | 1 | 1.8
  CCR3-mRNA | 0.644 | 0.372 | -0.0846 | 1.37 | 1.56 | 0.943 | 2.59 | 0.0866 | 1 | Wald | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR3 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa05203 |  | CCR3 | NA | azure4 | 1 | 1.73118279569892
  CXCR4-mRNA | 0.493 | 0.361 | -0.214 | 1.2 | 1.41 | 0.862 | 2.3 | 0.175 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR4 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa04670;hsa04672;hsa05200 |  | CXCR4 | NA | azure4 | 1 | 1.36565096952909
  CXCL5-mRNA | 0.527 | 0.494 | -0.441 | 1.5 | 1.44 | 0.737 | 2.82 | 0.288 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCL5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04668;hsa05133;hsa05323 |  | CXCL5 | NA | azure4 | 1 | 1.0668016194332
  CXCL8-mRNA | 0.57 | 0.644 | -0.693 | 1.83 | 1.48 | 0.619 | 3.56 | 0.378 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | CXCL8 | mRNA | 0 |  | Chemokine receptors bind chemokines;Senescence-Associated Secretory Phenotype (SASP);G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04072;hsa04620;hsa04621;hsa04622;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05142;hsa05144;hsa05146;hsa05160;hsa05161;hsa05164;hsa05200;hsa05202;hsa05219;hsa05323 |  | CXCL8 | NA | azure4 | 1 | 0.885093167701863
  Ccl3-mRNA | 0.368 | 0.434 | -0.483 | 1.22 | 1.29 | 0.715 | 2.33 | 0.399 | 1 | loglinear | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl3 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04620;hsa05132;hsa05142;hsa05323 |  | CCL3 | NA | azure4 | 1 | 0.847926267281106
  CXCR6-mRNA | 0.254 | 0.311 | -0.356 | 0.864 | 1.19 | 0.781 | 1.82 | 0.417 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR6 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CXCR6 | NA | azure4 | 1 | 0.816720257234727
  CCR5-mRNA | -0.0755 | 0.309 | -0.681 | 0.531 | 0.949 | 0.624 | 1.44 | 0.808 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa05145;hsa05203 |  | CCR5 | NA | azure4 | 1 | -0.244336569579288
  CCR2-mRNA | -0.00487 | 0.253 | -0.502 | 0.492 | 0.997 | 0.706 | 1.41 | 0.985 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR2 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CCR2 | NA | azure4 | 1 | -0.0192490118577075

  ##### DE Results - Chemokine receptors bind chemokines genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Costimulation by the CD28 family genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  BTLA-mRNA | 0.534 | 0.341 | -0.135 | 1.2 | 1.45 | 0.911 | 2.3 | 0.121 | 1 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | BTLA | mRNA | 0 |  | Costimulation by the CD28 family |  |  | BTLA | NA | azure4 | 1 | 1.56598240469208
  CD274-mRNA | 0.484 | 0.353 | -0.208 | 1.18 | 1.4 | 0.866 | 2.26 | 0.174 | 1 | Wald | Costimulation by the CD28 family | IMMUNOGC_C4839 | CD274 | mRNA | 0 |  | PD-1 signaling;Costimulation by the CD28 family | hsa04514 |  | CD274 | NA | azure4 | 1 | 1.37110481586402
  CD3G-mRNA | -0.324 | 0.306 | -0.924 | 0.275 | 0.799 | 0.527 | 1.21 | 0.292 | 1 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | CD3G | mRNA | 0 |  | Downstream TCR signaling;FCGR activation;Regulation of actin dynamics for phagocytic cup formation;Costimulation by the CD28 family | hsa04640;hsa04660;hsa05142;hsa05162;hsa05166 | T-cells | CD3G | NA | azure4 | 1 | -1.05882352941176
  PDCD1-mRNA | -0.263 | 0.334 | -0.919 | 0.392 | 0.833 | 0.529 | 1.31 | 0.433 | 1 | Wald | Costimulation by the CD28 family | IMMUNOGC_C4839 | PDCD1 | mRNA | 0 |  | PD-1 signaling;Costimulation by the CD28 family | hsa04514;hsa04660 |  | PDCD1 | NA | azure4 | 1 | -0.787425149700599
  ICOS-mRNA | -0.165 | 0.297 | -0.747 | 0.418 | 0.892 | 0.596 | 1.34 | 0.58 | 1 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | ICOS | mRNA | 0 |  | Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa05340 |  | ICOS | NA | azure4 | 1 | -0.555555555555556
  CD3E-mRNA | -0.142 | 0.297 | -0.725 | 0.44 | 0.906 | 0.605 | 1.36 | 0.633 | 1 | lm.nb | Costimulation by the CD28 family, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD3E | mRNA | 0 |  | Downstream TCR signaling;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Phosphorylation of CD3 and TCR zeta chains;Costimulation by the CD28 family | hsa04640;hsa04660;hsa05142;hsa05162;hsa05166;hsa05340 | T-cells | CD3E | NA | azure4 | 1 | -0.478114478114478
  CD4-mRNA | -0.0981 | 0.275 | -0.636 | 0.44 | 0.934 | 0.643 | 1.36 | 0.722 | 1 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | CD4 | mRNA | 0 |  | Nef Mediated CD4 Down-regulation;Binding and entry of HIV virion;Costimulation by the CD28 family | hsa04514;hsa04612;hsa04640;hsa04660;hsa05340 |  | CD4 | NA | azure4 | 1 | -0.356727272727273
  CTLA4-mRNA | -0.118 | 0.362 | -0.828 | 0.593 | 0.922 | 0.563 | 1.51 | 0.747 | 1 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | CTLA4 | mRNA | 0 |  | Costimulation by the CD28 family | hsa04514;hsa04660;hsa05320;hsa05323 |  | CTLA4 | NA | azure4 | 1 | -0.325966850828729
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Costimulation by the CD28 family genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - DAP12 interactions genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  Cd300lb-mRNA | 0.721 | 0.271 | 0.19 | 1.25 | 1.65 | 1.14 | 2.38 | 0.00913 | 0.738 | lm.nb | DAP12 interactions, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | Cd300lb | mRNA | 0 |  | DAP12 interactions;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |  |  | CD300LB | NA | azure4 | 1 | 2.66051660516605
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  KLRD1-mRNA | 0.0215 | 0.257 | -0.481 | 0.524 | 1.01 | 0.716 | 1.44 | 0.933 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | KLRD1 | mRNA | 0 |  | DAP12 signaling;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;DAP12 interactions | hsa04612;hsa04650;hsa05332 | Cytotoxic cells | KLRD1 | NA | azure4 | 1 | 0.0836575875486381
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - DAP12 interactions genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - DAP12 signaling genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  KLRD1-mRNA | 0.0215 | 0.257 | -0.481 | 0.524 | 1.01 | 0.716 | 1.44 | 0.933 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | KLRD1 | mRNA | 0 |  | DAP12 signaling;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;DAP12 interactions | hsa04612;hsa04650;hsa05332 | Cytotoxic cells | KLRD1 | NA | azure4 | 1 | 0.0836575875486381
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - DAP12 signaling genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Degradation of the extracellular matrix genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  ADAM9-mRNA | -0.442 | 0.342 | -1.11 | 0.229 | 0.736 | 0.462 | 1.17 | 0.2 | 1 | lm.nb | Degradation of the extracellular matrix | IMMUNOGC_C4839 | ADAM9 | mRNA | 0 |  | Degradation of the extracellular matrix |  |  | ADAM9 | NA | azure4 | 1 | -1.29239766081871
  TPSAB1-mRNA | 0.151 | 0.333 | -0.503 | 0.804 | 1.11 | 0.706 | 1.75 | 0.653 | 1 | Wald | Degradation of the extracellular matrix | IMMUNOGC_C4839 | TPSAB1 | mRNA | 0 |  | Degradation of the extracellular matrix |  | Mast cells | TPSAB1 | NA | azure4 | 1 | 0.453453453453453
  CTSG-mRNA | 0.0673 | 0.308 | -0.537 | 0.671 | 1.05 | 0.689 | 1.59 | 0.828 | 1 | Wald | Degradation of the extracellular matrix | IMMUNOGC_C4839 | CTSG | mRNA | 0 |  | Degradation of the extracellular matrix | hsa04080;hsa05146;hsa05322 |  | CTSG | NA | azure4 | 1 | 0.218506493506494

  ##### DE Results - Degradation of the extracellular matrix genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Downstream signal transduction genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  STAT6-mRNA | 0.248 | 0.414 | -0.564 | 1.06 | 1.19 | 0.677 | 2.09 | 0.55 | 1 | lm.nb | Downstream signal transduction, Signaling by PDGF | IMMUNOGC_C4839 | STAT6 | mRNA | 0 |  | Downstream signal transduction;Signaling by PDGF | hsa04630;hsa05161;hsa05321 |  | STAT6 | NA | azure4 | 1 | 0.599033816425121
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Downstream signal transduction genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - FCERI mediated MAPK activation genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  JUN-mRNA | 0.833 | 0.35 | 0.147 | 1.52 | 1.78 | 1.11 | 2.87 | 0.0194 | 1 | lm.nb | FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | JUN | mRNA | 0 |  | Pre-NOTCH Transcription and Translation;Oxidative Stress Induced Senescence;FCERI mediated MAPK activation;Senescence-Associated Secretory Phenotype (SASP);MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04012;hsa04024;hsa04380;hsa04510;hsa04620;hsa04660;hsa04662;hsa04668;hsa04722;hsa04912;hsa04915;hsa04921;hsa04932;hsa04933;hsa05120;hsa05132;hsa05133;hsa05140;hsa05142;hsa05161;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05203;hsa05210;hsa05211;hsa05231;hsa05321;hsa05323 |  | JUN | NA | azure4 | 1 | 2.38
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255

  ##### DE Results - FCERI mediated MAPK activation genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - G alpha (i) signalling events genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  FPR2-mRNA | 1.79 | 0.308 | 1.19 | 2.4 | 3.47 | 2.28 | 5.27 | 8.3e-08 | 3.73e-05 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | FPR2 | mRNA | 0 |  | G alpha (q) signalling events;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04080 |  | FPR2 | NA | slateblue2 | 16 | 5.81168831168831
  Cxcl10-mRNA | 0.621 | 0.345 | -0.055 | 1.3 | 1.54 | 0.963 | 2.46 | 0.075 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Cxcl10 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04620;hsa04622;hsa04623;hsa04668;hsa05164 |  | CXCL10 | NA | azure4 | 1 | 1.8
  CCR3-mRNA | 0.644 | 0.372 | -0.0846 | 1.37 | 1.56 | 0.943 | 2.59 | 0.0866 | 1 | Wald | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR3 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa05203 |  | CCR3 | NA | azure4 | 1 | 1.73118279569892
  PMCH-mRNA | -0.495 | 0.289 | -1.06 | 0.0726 | 0.71 | 0.479 | 1.05 | 0.0908 | 1 | Wald | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | PMCH | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events |  |  | PMCH | NA | azure4 | 1 | -1.71280276816609
  CXCR4-mRNA | 0.493 | 0.361 | -0.214 | 1.2 | 1.41 | 0.862 | 2.3 | 0.175 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR4 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa04670;hsa04672;hsa05200 |  | CXCR4 | NA | azure4 | 1 | 1.36565096952909
  CXCL5-mRNA | 0.527 | 0.494 | -0.441 | 1.5 | 1.44 | 0.737 | 2.82 | 0.288 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCL5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04668;hsa05133;hsa05323 |  | CXCL5 | NA | azure4 | 1 | 1.0668016194332
  PTGDR2-mRNA | 0.29 | 0.319 | -0.336 | 0.916 | 1.22 | 0.792 | 1.89 | 0.366 | 1 | lm.nb | G alpha (i) signalling events | IMMUNOGC_C4839 | PTGDR2 | mRNA | 0 |  | G alpha (i) signalling events |  |  | PTGDR2 | NA | azure4 | 1 | 0.909090909090909
  CXCL8-mRNA | 0.57 | 0.644 | -0.693 | 1.83 | 1.48 | 0.619 | 3.56 | 0.378 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | CXCL8 | mRNA | 0 |  | Chemokine receptors bind chemokines;Senescence-Associated Secretory Phenotype (SASP);G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04072;hsa04620;hsa04621;hsa04622;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05142;hsa05144;hsa05146;hsa05160;hsa05161;hsa05164;hsa05200;hsa05202;hsa05219;hsa05323 |  | CXCL8 | NA | azure4 | 1 | 0.885093167701863
  CXCR6-mRNA | 0.254 | 0.311 | -0.356 | 0.864 | 1.19 | 0.781 | 1.82 | 0.417 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR6 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CXCR6 | NA | azure4 | 1 | 0.816720257234727
  NMUR1-mRNA | -0.162 | 0.317 | -0.783 | 0.46 | 0.894 | 0.581 | 1.38 | 0.611 | 1 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | NMUR1 | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events | hsa04080 |  | NMUR1 | NA | azure4 | 1 | -0.511041009463722
  TAS2R38-mRNA | -0.0959 | 0.344 | -0.771 | 0.579 | 0.936 | 0.586 | 1.49 | 0.781 | 1 | Wald | G alpha (i) signalling events | IMMUNOGC_C4839 | TAS2R38 | mRNA | 0 |  | G alpha (i) signalling events |  |  | TAS2R38 | NA | azure4 | 1 | -0.278779069767442
  CCR5-mRNA | -0.0755 | 0.309 | -0.681 | 0.531 | 0.949 | 0.624 | 1.44 | 0.808 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa05145;hsa05203 |  | CCR5 | NA | azure4 | 1 | -0.244336569579288
  CCR2-mRNA | -0.00487 | 0.253 | -0.502 | 0.492 | 0.997 | 0.706 | 1.41 | 0.985 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR2 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CCR2 | NA | azure4 | 1 | -0.0192490118577075

  ##### DE Results - G alpha (i) signalling events genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - G alpha (q) signalling events genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  FPR2-mRNA | 1.79 | 0.308 | 1.19 | 2.4 | 3.47 | 2.28 | 5.27 | 8.3e-08 | 3.73e-05 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | FPR2 | mRNA | 0 |  | G alpha (q) signalling events;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04080 |  | FPR2 | NA | slateblue2 | 16 | 5.81168831168831
  TRIO-mRNA | 0.653 | 0.298 | 0.0698 | 1.24 | 1.57 | 1.05 | 2.36 | 0.0307 | 1 | lm.nb | G alpha (q) signalling events | IMMUNOGC_C4839 | TRIO | mRNA | 0 |  | G alpha (q) signalling events |  |  | TRIO | NA | azure4 | 1 | 2.19127516778524
  PMCH-mRNA | -0.495 | 0.289 | -1.06 | 0.0726 | 0.71 | 0.479 | 1.05 | 0.0908 | 1 | Wald | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | PMCH | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events |  |  | PMCH | NA | azure4 | 1 | -1.71280276816609
  NMUR1-mRNA | -0.162 | 0.317 | -0.783 | 0.46 | 0.894 | 0.581 | 1.38 | 0.611 | 1 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | NMUR1 | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events | hsa04080 |  | NMUR1 | NA | azure4 | 1 | -0.511041009463722
  ANXA1-mRNA | -0.00907 | 0.253 | -0.506 | 0.488 | 0.994 | 0.704 | 1.4 | 0.972 | 1 | lm.nb | G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | ANXA1 | mRNA | 0 |  | G alpha (q) signalling events;Formyl peptide receptors bind formyl peptides and many other ligands;Peptide ligand-binding receptors |  |  | ANXA1 | NA | azure4 | 1 | -0.0358498023715415

  ##### DE Results - G alpha (q) signalling events genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - G beta.CL.gamma signalling through PI3Kgamma genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473

  ##### DE Results - G beta.CL.gamma signalling through PI3Kgamma genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Generic Transcription Pathway genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  RORC-mRNA | 0.328 | 0.336 | -0.331 | 0.987 | 1.26 | 0.795 | 1.98 | 0.331 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | RORC | mRNA | 0 |  | Generic Transcription Pathway | hsa05321 |  | RORC | NA | azure4 | 1 | 0.976190476190476
  NR3C1-mRNA | 0.226 | 0.26 | -0.285 | 0.736 | 1.17 | 0.821 | 1.67 | 0.388 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | NR3C1 | mRNA | 0 |  | Generic Transcription Pathway | hsa04080 |  | NR3C1 | NA | azure4 | 1 | 0.869230769230769
  SMAD2-mRNA | 0.19 | 0.295 | -0.387 | 0.767 | 1.14 | 0.764 | 1.7 | 0.521 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | SMAD2 | mRNA | 0 |  | Generic Transcription Pathway | hsa04068;hsa04110;hsa04144;hsa04350;hsa04390;hsa04550;hsa04933;hsa05142;hsa05166;hsa05200;hsa05205;hsa05210;hsa05212;hsa05321 |  | SMAD2 | NA | azure4 | 1 | 0.64406779661017
  Junb-mRNA | 0.254 | 0.45 | -0.628 | 1.14 | 1.19 | 0.647 | 2.2 | 0.574 | 1 | loglinear | Generic Transcription Pathway | IMMUNOGC_C4839 | Junb | mRNA | 0 |  | Generic Transcription Pathway | hsa04380;hsa04668 |  | JUNB | NA | azure4 | 1 | 0.564444444444444
  Ddit4-mRNA | -0.154 | 0.353 | -0.846 | 0.539 | 0.899 | 0.556 | 1.45 | 0.664 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | Ddit4 | mRNA | 0 |  | Generic Transcription Pathway | hsa04150;hsa04151;hsa05206 |  | DDIT4 | NA | azure4 | 1 | -0.436260623229462
  PRKAA1-mRNA | 0.0827 | 0.273 | -0.452 | 0.617 | 1.06 | 0.731 | 1.53 | 0.762 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | PRKAA1 | mRNA | 0 |  | Generic Transcription Pathway | hsa04068;hsa04150;hsa04151;hsa04910;hsa04920;hsa04921;hsa04931;hsa04932;hsa05410 |  | PRKAA1 | NA | azure4 | 1 | 0.302930402930403
  G6PD-mRNA | 0.0687 | 0.387 | -0.69 | 0.827 | 1.05 | 0.62 | 1.77 | 0.86 | 1 | lm.nb | Generic Transcription Pathway, Metabolism of carbohydrates | IMMUNOGC_C4839 | G6PD | mRNA | 0 |  | Generic Transcription Pathway;Metabolism of carbohydrates | hsa01100;hsa05230 |  | G6PD | NA | azure4 | 1 | 0.177519379844961
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Generic Transcription Pathway genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - GPVI-mediated activation cascade genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - GPVI-mediated activation cascade genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  Cd300lb-mRNA | 0.721 | 0.271 | 0.19 | 1.25 | 1.65 | 1.14 | 2.38 | 0.00913 | 0.738 | lm.nb | DAP12 interactions, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | Cd300lb | mRNA | 0 |  | DAP12 interactions;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |  |  | CD300LB | NA | azure4 | 1 | 2.66051660516605
  CD33-mRNA | 0.535 | 0.275 | -0.00451 | 1.07 | 1.45 | 0.997 | 2.11 | 0.055 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD33 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04640 |  | CD33 | NA | azure4 | 1 | 1.94545454545455
  KLRF1-mRNA | -0.274 | 0.259 | -0.783 | 0.234 | 0.827 | 0.581 | 1.18 | 0.293 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | KLRF1 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |  |  | KLRF1 | NA | azure4 | 1 | -1.05791505791506
  NCR1-mRNA | 0.294 | 0.319 | -0.33 | 0.918 | 1.23 | 0.795 | 1.89 | 0.359 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | NCR1 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04650 | NK cells | NCR1 | NA | azure4 | 1 | 0.921630094043887
  CD8B-mRNA | -0.307 | 0.337 | -0.967 | 0.353 | 0.808 | 0.512 | 1.28 | 0.365 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD8B | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04514;hsa04612;hsa04640;hsa04660;hsa05340 | CD8 T cells | CD8B | NA | azure4 | 1 | -0.910979228486647
  KIR3DL1-mRNA | 0.252 | 0.361 | -0.456 | 0.96 | 1.19 | 0.729 | 1.95 | 0.487 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | KIR3DL1 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04612;hsa04650;hsa05332 | NK CD56dim cells | KIR3DL1 | NA | azure4 | 1 | 0.698060941828255
  LAIR2-mRNA | -0.223 | 0.356 | -0.921 | 0.474 | 0.857 | 0.528 | 1.39 | 0.532 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | LAIR2 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |  |  | LAIR2 | NA | azure4 | 1 | -0.626404494382023
  CD62L-mRNA | 0.177 | 0.356 | -0.52 | 0.875 | 1.13 | 0.697 | 1.83 | 0.619 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD62L | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04514 |  | SELL | NA | azure4 | 1 | 0.497191011235955
  CD3E-mRNA | -0.142 | 0.297 | -0.725 | 0.44 | 0.906 | 0.605 | 1.36 | 0.633 | 1 | lm.nb | Costimulation by the CD28 family, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD3E | mRNA | 0 |  | Downstream TCR signaling;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Phosphorylation of CD3 and TCR zeta chains;Costimulation by the CD28 family | hsa04640;hsa04660;hsa05142;hsa05162;hsa05166;hsa05340 | T-cells | CD3E | NA | azure4 | 1 | -0.478114478114478
  CD40-mRNA | 0.18 | 0.396 | -0.596 | 0.957 | 1.13 | 0.662 | 1.94 | 0.65 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, TNFR2 non-canonical NF-kB pathway | IMMUNOGC_C4839 | CD40 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04514;hsa04620;hsa04672;hsa05144;hsa05145;hsa05166;hsa05169;hsa05202;hsa05310;hsa05320;hsa05322;hsa05330;hsa05340;hsa05416 |  | CD40 | NA | azure4 | 1 | 0.454545454545455
  CD160-mRNA | 0.106 | 0.247 | -0.377 | 0.589 | 1.08 | 0.77 | 1.5 | 0.669 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD160 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell |  |  | CD160 | NA | azure4 | 1 | 0.42914979757085
  CD8A-mRNA | -0.153 | 0.389 | -0.915 | 0.609 | 0.899 | 0.53 | 1.52 | 0.694 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | CD8A | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | hsa04514;hsa04612;hsa04640;hsa04660;hsa05340 | CD8 T cells | CD8A | NA | azure4 | 1 | -0.393316195372751
  CD40LG-mRNA | -0.0315 | 0.301 | -0.622 | 0.559 | 0.978 | 0.65 | 1.47 | 0.917 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, TNFR2 non-canonical NF-kB pathway | IMMUNOGC_C4839 | CD40LG | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04514;hsa04660;hsa04672;hsa05144;hsa05145;hsa05310;hsa05320;hsa05322;hsa05330;hsa05340;hsa05416 |  | CD40LG | NA | azure4 | 1 | -0.104651162790698
  KLRD1-mRNA | 0.0215 | 0.257 | -0.481 | 0.524 | 1.01 | 0.716 | 1.44 | 0.933 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | IMMUNOGC_C4839 | KLRD1 | mRNA | 0 |  | DAP12 signaling;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;DAP12 interactions | hsa04612;hsa04650;hsa05332 | Cytotoxic cells | KLRD1 | NA | azure4 | 1 | 0.0836575875486381

  ##### DE Results - Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Interleukin-1 signaling genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  Il1rn-mRNA | 2.77 | 0.396 | 1.99 | 3.55 | 6.82 | 3.98 | 11.7 | 3.92e-10 | 2.64e-07 | lm.nb | Interleukin-1 signaling | IMMUNOGC_C4839 | Il1rn | mRNA | 0 |  | Interleukin-1 signaling |  |  | IL1RN | NA | slateblue1 | 16 | 6.99494949494949
  IL1B-mRNA | 0.413 | 0.422 | -0.414 | 1.24 | 1.33 | 0.751 | 2.36 | 0.33 | 1 | loglinear | Interleukin-1 signaling | IMMUNOGC_C4839 | IL1B | mRNA | 0 |  | Interleukin-1 signaling;CLEC7A (Dectin-1) signaling | hsa04010;hsa04060;hsa04064;hsa04210;hsa04380;hsa04620;hsa04621;hsa04623;hsa04640;hsa04668;hsa04750;hsa04932;hsa04933;hsa04940;hsa05010;hsa05020;hsa05132;hsa05133;hsa05134;hsa05140;hsa05142;hsa05143;hsa05144;hsa05146;hsa05152;hsa05162;hsa05164;hsa05168;hsa05321;hsa05323;hsa05332 |  | IL1B | NA | azure4 | 1 | 0.97867298578199
  NFKB1-mRNA | 0.24 | 0.266 | -0.281 | 0.76 | 1.18 | 0.823 | 1.69 | 0.369 | 1 | lm.nb | Interleukin-1 signaling, MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | NFKB1 | mRNA | 0 |  | TRAF6 mediated NF-kB activation;CD209 (DC-SIGN) signaling;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;CLEC7A (Dectin-1) signaling;Interleukin-1 signaling;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04014;hsa04024;hsa04062;hsa04064;hsa04066;hsa04071;hsa04151;hsa04210;hsa04380;hsa04620;hsa04621;hsa04622;hsa04623;hsa04660;hsa04662;hsa04668;hsa04722;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05140;hsa05142;hsa05145;hsa05146;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05202;hsa05203;hsa05206;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05321 |  | NFKB1 | NA | azure4 | 1 | 0.902255639097744
  IL1R2-mRNA | 0.49 | 0.546 | -0.579 | 1.56 | 1.4 | 0.669 | 2.95 | 0.371 | 1 | loglinear | Interleukin-1 signaling | IMMUNOGC_C4839 | IL1R2 | mRNA | 0 |  | Interleukin-1 signaling | hsa04010;hsa04060;hsa04640;hsa05146;hsa05166;hsa05202 |  | IL1R2 | NA | azure4 | 1 | 0.897435897435897
  TOLLIP-mRNA | -0.0768 | 0.304 | -0.672 | 0.519 | 0.948 | 0.628 | 1.43 | 0.801 | 1 | lm.nb | Interleukin-1 signaling | IMMUNOGC_C4839 | TOLLIP | mRNA | 0 |  | Interleukin-1 signaling | hsa04620 |  | TOLLIP | NA | azure4 | 1 | -0.252631578947368

  ##### DE Results - Interleukin-1 signaling genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Metabolism of carbohydrates genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  Pfkfb3-mRNA | 0.978 | 0.369 | 0.255 | 1.7 | 1.97 | 1.19 | 3.25 | 0.00939 | 0.738 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | Pfkfb3 | mRNA | 0 |  | Metabolism of carbohydrates | hsa04066 |  | PFKFB3 | NA | azure4 | 1 | 2.65040650406504
  HPSE-mRNA | 0.666 | 0.265 | 0.147 | 1.19 | 1.59 | 1.11 | 2.27 | 0.0137 | 0.963 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | HPSE | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100;hsa05205 |  | HPSE | NA | azure4 | 1 | 2.51320754716981
  NUP107-mRNA | 0.41 | 0.282 | -0.142 | 0.963 | 1.33 | 0.906 | 1.95 | 0.149 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | NUP107 | mRNA | 0 |  | Metabolism of carbohydrates |  |  | NUP107 | NA | azure4 | 1 | 1.45390070921986
  CHIT1-mRNA | 0.408 | 0.426 | -0.426 | 1.24 | 1.33 | 0.744 | 2.37 | 0.34 | 1 | Wald | Metabolism of carbohydrates | IMMUNOGC_C4839 | CHIT1 | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100 |  | CHIT1 | NA | azure4 | 1 | 0.957746478873239
  GUSB-mRNA | -0.142 | 0.302 | -0.733 | 0.45 | 0.906 | 0.602 | 1.37 | 0.64 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | GUSB | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100 |  | GUSB | NA | azure4 | 1 | -0.470198675496689
  GAPDH-mRNA | -0.112 | 0.295 | -0.689 | 0.465 | 0.925 | 0.62 | 1.38 | 0.705 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | GAPDH | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100;hsa04066;hsa05010 |  | GAPDH | NA | azure4 | 1 | -0.379661016949153
  G6PD-mRNA | 0.0687 | 0.387 | -0.69 | 0.827 | 1.05 | 0.62 | 1.77 | 0.86 | 1 | lm.nb | Generic Transcription Pathway, Metabolism of carbohydrates | IMMUNOGC_C4839 | G6PD | mRNA | 0 |  | Generic Transcription Pathway;Metabolism of carbohydrates | hsa01100;hsa05230 |  | G6PD | NA | azure4 | 1 | 0.177519379844961

  ##### DE Results - Metabolism of carbohydrates genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - MicroRNA (miRNA) biogenesis genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  DICER1-mRNA | 0.256 | 0.354 | -0.437 | 0.949 | 1.19 | 0.739 | 1.93 | 0.47 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DICER1 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis | hsa05206 |  | DICER1 | NA | azure4 | 1 | 0.72316384180791
  DGCR8-mRNA | -0.209 | 0.398 | -0.989 | 0.571 | 0.865 | 0.504 | 1.49 | 0.601 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DGCR8 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | DGCR8 | NA | azure4 | 1 | -0.525125628140704
  DROSHA-mRNA | 0.147 | 0.3 | -0.441 | 0.735 | 1.11 | 0.737 | 1.66 | 0.626 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DROSHA | mRNA | 0 |  | MicroRNA (miRNA) biogenesis | hsa05205 |  | DROSHA | NA | azure4 | 1 | 0.49
  XPO5-mRNA | 0.126 | 0.301 | -0.463 | 0.715 | 1.09 | 0.725 | 1.64 | 0.677 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | XPO5 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | XPO5 | NA | azure4 | 1 | 0.418604651162791
  TARBP2-mRNA | 0.0141 | 0.32 | -0.613 | 0.642 | 1.01 | 0.654 | 1.56 | 0.965 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | TARBP2 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | TARBP2 | NA | azure4 | 1 | 0.0440625

  ##### DE Results - MicroRNA (miRNA) biogenesis genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - MyD88.CL.Mal cascade initiated on plasma membrane genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  JUN-mRNA | 0.833 | 0.35 | 0.147 | 1.52 | 1.78 | 1.11 | 2.87 | 0.0194 | 1 | lm.nb | FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | JUN | mRNA | 0 |  | Pre-NOTCH Transcription and Translation;Oxidative Stress Induced Senescence;FCERI mediated MAPK activation;Senescence-Associated Secretory Phenotype (SASP);MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04012;hsa04024;hsa04380;hsa04510;hsa04620;hsa04660;hsa04662;hsa04668;hsa04722;hsa04912;hsa04915;hsa04921;hsa04932;hsa04933;hsa05120;hsa05132;hsa05133;hsa05140;hsa05142;hsa05161;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05203;hsa05210;hsa05211;hsa05231;hsa05321;hsa05323 |  | JUN | NA | azure4 | 1 | 2.38
  NFKBIA-mRNA | 0.467 | 0.388 | -0.293 | 1.23 | 1.38 | 0.816 | 2.34 | 0.231 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | NFKBIA | mRNA | 0 |  | RIP-mediated NFkB activation via ZBP1;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04024;hsa04062;hsa04064;hsa04210;hsa04380;hsa04620;hsa04621;hsa04622;hsa04623;hsa04660;hsa04662;hsa04668;hsa04722;hsa04920;hsa04931;hsa05120;hsa05131;hsa05134;hsa05140;hsa05142;hsa05145;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05203;hsa05215;hsa05220;hsa05222 |  | NFKBIA | NA | azure4 | 1 | 1.20360824742268
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  MAPK14-mRNA | 0.307 | 0.317 | -0.315 | 0.929 | 1.24 | 0.804 | 1.9 | 0.336 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | MAPK14 | mRNA | 0 |  | NOD12 Signaling Pathway;ERKMAPK targets;p38MAPK events;activated TAK1 mediates p38 MAPK activation;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04015;hsa04068;hsa04071;hsa04261;hsa04370;hsa04380;hsa04550;hsa04611;hsa04620;hsa04621;hsa04622;hsa04660;hsa04664;hsa04668;hsa04670;hsa04722;hsa04723;hsa04728;hsa04750;hsa04912;hsa04914;hsa04917;hsa04933;hsa05014;hsa05120;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05164;hsa05169;hsa05205 |  | MAPK14 | NA | azure4 | 1 | 0.968454258675079
  NFKB1-mRNA | 0.24 | 0.266 | -0.281 | 0.76 | 1.18 | 0.823 | 1.69 | 0.369 | 1 | lm.nb | Interleukin-1 signaling, MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | NFKB1 | mRNA | 0 |  | TRAF6 mediated NF-kB activation;CD209 (DC-SIGN) signaling;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;CLEC7A (Dectin-1) signaling;Interleukin-1 signaling;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04014;hsa04024;hsa04062;hsa04064;hsa04066;hsa04071;hsa04151;hsa04210;hsa04380;hsa04620;hsa04621;hsa04622;hsa04623;hsa04660;hsa04662;hsa04668;hsa04722;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05140;hsa05142;hsa05145;hsa05146;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05202;hsa05203;hsa05206;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05321 |  | NFKB1 | NA | azure4 | 1 | 0.902255639097744
  RELA-mRNA | 0.245 | 0.287 | -0.316 | 0.807 | 1.19 | 0.803 | 1.75 | 0.394 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | RELA | mRNA | 0 |  | TRAF6 mediated NF-kB activation;CD209 (DC-SIGN) signaling;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;CLEC7A (Dectin-1) signaling;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04014;hsa04024;hsa04062;hsa04064;hsa04066;hsa04071;hsa04151;hsa04210;hsa04380;hsa04620;hsa04621;hsa04622;hsa04623;hsa04660;hsa04662;hsa04668;hsa04722;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05140;hsa05142;hsa05145;hsa05146;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05202;hsa05203;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05321 |  | RELA | NA | azure4 | 1 | 0.853658536585366
  MAPK8-mRNA | 0.181 | 0.291 | -0.39 | 0.751 | 1.13 | 0.763 | 1.68 | 0.536 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane | IMMUNOGC_C4839 | MAPK8 | mRNA | 0 |  | Activation of the AP-1 family of transcription factors;DSCAM interactions;Activation of BMF and translocation to mitochondria;JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04012;hsa04014;hsa04024;hsa04068;hsa04071;hsa04380;hsa04510;hsa04620;hsa04621;hsa04622;hsa04664;hsa04668;hsa04722;hsa04723;hsa04728;hsa04750;hsa04910;hsa04912;hsa04914;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05210;hsa05212;hsa05231 |  | MAPK8 | NA | azure4 | 1 | 0.621993127147766
  MAPK11-mRNA | 0.205 | 0.337 | -0.457 | 0.866 | 1.15 | 0.729 | 1.82 | 0.546 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | MAPK11 | mRNA | 0 |  | Activation of the AP-1 family of transcription factors;ERKMAPK targets;VEGFA-VEGFR2 Pathway;activated TAK1 mediates p38 MAPK activation;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04015;hsa04068;hsa04071;hsa04261;hsa04370;hsa04380;hsa04550;hsa04611;hsa04620;hsa04621;hsa04622;hsa04660;hsa04664;hsa04668;hsa04670;hsa04722;hsa04723;hsa04728;hsa04750;hsa04912;hsa04914;hsa04917;hsa04933;hsa05014;hsa05120;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05164;hsa05169;hsa05205 |  | MAPK11 | NA | azure4 | 1 | 0.608308605341246

  ##### DE Results - MyD88.CL.Mal cascade initiated on plasma membrane genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Peptide ligand-binding receptors genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  FPR2-mRNA | 1.79 | 0.308 | 1.19 | 2.4 | 3.47 | 2.28 | 5.27 | 8.3e-08 | 3.73e-05 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | FPR2 | mRNA | 0 |  | G alpha (q) signalling events;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04080 |  | FPR2 | NA | slateblue2 | 16 | 5.81168831168831
  Ccl2-mRNA | -0.471 | 0.17 | -0.804 | -0.138 | 0.722 | 0.573 | 0.909 | 0.00677 | 0.738 | Wald | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl2 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04621;hsa04668;hsa04933;hsa05142;hsa05144;hsa05164;hsa05168;hsa05323 |  | CCL2 | NA | azure4 | 1 | -2.77058823529412
  Ccl4-mRNA | 0.936 | 0.396 | 0.16 | 1.71 | 1.91 | 1.12 | 3.28 | 0.0202 | 1 | lm.nb | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl4 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04620;hsa04623;hsa05132 |  | CCL4 | NA | azure4 | 1 | 2.36363636363636
  Cxcl10-mRNA | 0.621 | 0.345 | -0.055 | 1.3 | 1.54 | 0.963 | 2.46 | 0.075 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Cxcl10 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04620;hsa04622;hsa04623;hsa04668;hsa05164 |  | CXCL10 | NA | azure4 | 1 | 1.8
  CCR3-mRNA | 0.644 | 0.372 | -0.0846 | 1.37 | 1.56 | 0.943 | 2.59 | 0.0866 | 1 | Wald | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR3 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa05203 |  | CCR3 | NA | azure4 | 1 | 1.73118279569892
  PMCH-mRNA | -0.495 | 0.289 | -1.06 | 0.0726 | 0.71 | 0.479 | 1.05 | 0.0908 | 1 | Wald | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | PMCH | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events |  |  | PMCH | NA | azure4 | 1 | -1.71280276816609
  CXCR4-mRNA | 0.493 | 0.361 | -0.214 | 1.2 | 1.41 | 0.862 | 2.3 | 0.175 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR4 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa04670;hsa04672;hsa05200 |  | CXCR4 | NA | azure4 | 1 | 1.36565096952909
  CXCL5-mRNA | 0.527 | 0.494 | -0.441 | 1.5 | 1.44 | 0.737 | 2.82 | 0.288 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCL5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04668;hsa05133;hsa05323 |  | CXCL5 | NA | azure4 | 1 | 1.0668016194332
  CXCL8-mRNA | 0.57 | 0.644 | -0.693 | 1.83 | 1.48 | 0.619 | 3.56 | 0.378 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | CXCL8 | mRNA | 0 |  | Chemokine receptors bind chemokines;Senescence-Associated Secretory Phenotype (SASP);G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04072;hsa04620;hsa04621;hsa04622;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05142;hsa05144;hsa05146;hsa05160;hsa05161;hsa05164;hsa05200;hsa05202;hsa05219;hsa05323 |  | CXCL8 | NA | azure4 | 1 | 0.885093167701863
  Ccl3-mRNA | 0.368 | 0.434 | -0.483 | 1.22 | 1.29 | 0.715 | 2.33 | 0.399 | 1 | loglinear | Chemokine receptors bind chemokines, Peptide ligand-binding receptors | IMMUNOGC_C4839 | Ccl3 | mRNA | 0 |  | Chemokine receptors bind chemokines;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04620;hsa05132;hsa05142;hsa05323 |  | CCL3 | NA | azure4 | 1 | 0.847926267281106
  CXCR6-mRNA | 0.254 | 0.311 | -0.356 | 0.864 | 1.19 | 0.781 | 1.82 | 0.417 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CXCR6 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CXCR6 | NA | azure4 | 1 | 0.816720257234727
  NMUR1-mRNA | -0.162 | 0.317 | -0.783 | 0.46 | 0.894 | 0.581 | 1.38 | 0.611 | 1 | lm.nb | G alpha (i) signalling events, G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | NMUR1 | mRNA | 0 |  | G alpha (q) signalling events;Peptide ligand-binding receptors;G alpha (i) signalling events | hsa04080 |  | NMUR1 | NA | azure4 | 1 | -0.511041009463722
  CCR5-mRNA | -0.0755 | 0.309 | -0.681 | 0.531 | 0.949 | 0.624 | 1.44 | 0.808 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR5 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04144;hsa05145;hsa05203 |  | CCR5 | NA | azure4 | 1 | -0.244336569579288
  ANXA1-mRNA | -0.00907 | 0.253 | -0.506 | 0.488 | 0.994 | 0.704 | 1.4 | 0.972 | 1 | lm.nb | G alpha (q) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | ANXA1 | mRNA | 0 |  | G alpha (q) signalling events;Formyl peptide receptors bind formyl peptides and many other ligands;Peptide ligand-binding receptors |  |  | ANXA1 | NA | azure4 | 1 | -0.0358498023715415
  CCR2-mRNA | -0.00487 | 0.253 | -0.502 | 0.492 | 0.997 | 0.706 | 1.41 | 0.985 | 1 | lm.nb | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors | IMMUNOGC_C4839 | CCR2 | mRNA | 0 |  | Chemokine receptors bind chemokines;G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062 |  | CCR2 | NA | azure4 | 1 | -0.0192490118577075

  ##### DE Results - Peptide ligand-binding receptors genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - RAF-independent MAPK13 activation genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL6-mRNA | 0.569 | 0.231 | 0.117 | 1.02 | 1.48 | 1.08 | 2.03 | 0.0155 | 0.973 | Wald | RAF-independent MAPK13 activation, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | IL6 | mRNA | 0 |  | Senescence-Associated Secretory Phenotype (SASP);RAF-independent MAPK13 activation | hsa04060;hsa04066;hsa04068;hsa04151;hsa04620;hsa04621;hsa04623;hsa04630;hsa04640;hsa04668;hsa04672;hsa04931;hsa04932;hsa04933;hsa05020;hsa05132;hsa05133;hsa05134;hsa05142;hsa05143;hsa05144;hsa05146;hsa05152;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05200;hsa05202;hsa05321;hsa05323;hsa05332;hsa05410 |  | IL6 | NA | azure4 | 1 | 2.46320346320346
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255

  ##### DE Results - RAF-independent MAPK13 activation genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - RAFMAP kinase cascade genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255

  ##### DE Results - RAFMAP kinase cascade genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Role of LAT2NTALLAB on calcium mobilization genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  MS4A2-mRNA | 0.33 | 0.447 | -0.546 | 1.21 | 1.26 | 0.685 | 2.31 | 0.462 | 1 | Wald | Role of LAT2NTALLAB on calcium mobilization | IMMUNOGC_C4839 | MS4A2 | mRNA | 0 |  | FCERI mediated Ca.PLS.2 mobilization;Role of LAT2NTALLAB on calcium mobilization | hsa04071;hsa04072;hsa04664;hsa05310 | Mast cells | MS4A2 | NA | azure4 | 1 | 0.738255033557047
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Role of LAT2NTALLAB on calcium mobilization genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Senescence-Associated Secretory Phenotype (SASP) genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  CEBPB-mRNA | 1.09 | 0.256 | 0.59 | 1.6 | 2.13 | 1.51 | 3.02 | 4.82e-05 | 0.0163 | lm.nb | Senescence-Associated Secretory Phenotype (SASP), Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | CEBPB | mRNA | 0 |  | Transcriptional regulation of white adipocyte differentiation;Senescence-Associated Secretory Phenotype (SASP) | hsa04668;hsa05152;hsa05202 |  | CEBPB | NA | slateblue4 | 16 | 4.2578125
  IL6-mRNA | 0.569 | 0.231 | 0.117 | 1.02 | 1.48 | 1.08 | 2.03 | 0.0155 | 0.973 | Wald | RAF-independent MAPK13 activation, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | IL6 | mRNA | 0 |  | Senescence-Associated Secretory Phenotype (SASP);RAF-independent MAPK13 activation | hsa04060;hsa04066;hsa04068;hsa04151;hsa04620;hsa04621;hsa04623;hsa04630;hsa04640;hsa04668;hsa04672;hsa04931;hsa04932;hsa04933;hsa05020;hsa05132;hsa05133;hsa05134;hsa05142;hsa05143;hsa05144;hsa05146;hsa05152;hsa05161;hsa05162;hsa05164;hsa05166;hsa05168;hsa05200;hsa05202;hsa05321;hsa05323;hsa05332;hsa05410 |  | IL6 | NA | azure4 | 1 | 2.46320346320346
  JUN-mRNA | 0.833 | 0.35 | 0.147 | 1.52 | 1.78 | 1.11 | 2.87 | 0.0194 | 1 | lm.nb | FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | JUN | mRNA | 0 |  | Pre-NOTCH Transcription and Translation;Oxidative Stress Induced Senescence;FCERI mediated MAPK activation;Senescence-Associated Secretory Phenotype (SASP);MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04012;hsa04024;hsa04380;hsa04510;hsa04620;hsa04660;hsa04662;hsa04668;hsa04722;hsa04912;hsa04915;hsa04921;hsa04932;hsa04933;hsa05120;hsa05132;hsa05133;hsa05140;hsa05142;hsa05161;hsa05164;hsa05166;hsa05168;hsa05169;hsa05200;hsa05203;hsa05210;hsa05211;hsa05231;hsa05321;hsa05323 |  | JUN | NA | azure4 | 1 | 2.38
  CXCL8-mRNA | 0.57 | 0.644 | -0.693 | 1.83 | 1.48 | 0.619 | 3.56 | 0.378 | 1 | loglinear | Chemokine receptors bind chemokines, G alpha (i) signalling events, Peptide ligand-binding receptors, Senescence-Associated Secretory Phenotype (SASP) | IMMUNOGC_C4839 | CXCL8 | mRNA | 0 |  | Chemokine receptors bind chemokines;Senescence-Associated Secretory Phenotype (SASP);G alpha (i) signalling events;Peptide ligand-binding receptors | hsa04060;hsa04062;hsa04064;hsa04072;hsa04620;hsa04621;hsa04622;hsa04932;hsa04933;hsa05120;hsa05131;hsa05132;hsa05133;hsa05134;hsa05142;hsa05144;hsa05146;hsa05160;hsa05161;hsa05164;hsa05200;hsa05202;hsa05219;hsa05323 |  | CXCL8 | NA | azure4 | 1 | 0.885093167701863

  ##### DE Results - Senescence-Associated Secretory Phenotype (SASP) genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Signaling by PDGF genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  STAT6-mRNA | 0.248 | 0.414 | -0.564 | 1.06 | 1.19 | 0.677 | 2.09 | 0.55 | 1 | lm.nb | Downstream signal transduction, Signaling by PDGF | IMMUNOGC_C4839 | STAT6 | mRNA | 0 |  | Downstream signal transduction;Signaling by PDGF | hsa04630;hsa05161;hsa05321 |  | STAT6 | NA | azure4 | 1 | 0.599033816425121
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  THBS1-mRNA | 0.212 | 0.462 | -0.693 | 1.12 | 1.16 | 0.619 | 2.17 | 0.647 | 1 | loglinear | Signaling by PDGF | IMMUNOGC_C4839 | THBS1 | mRNA | 0 |  | Signaling by PDGF;O-glycosylation of TSR domain-containing proteins | hsa04015;hsa04145;hsa04151;hsa04350;hsa04510;hsa05144;hsa05205;hsa05206;hsa05219 |  | THBS1 | NA | azure4 | 1 | 0.458874458874459
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Signaling by PDGF genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Signaling by SCF-KIT genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  AGO2-mRNA | 0.439 | 0.329 | -0.205 | 1.08 | 1.36 | 0.867 | 2.12 | 0.185 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | AGO2 | mRNA | 0 |  | Small interfering RNA (siRNA) biogenesis;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions |  |  | AGO2 | NA | azure4 | 1 | 1.33434650455927
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  CD28-mRNA | -0.06 | 0.281 | -0.61 | 0.49 | 0.959 | 0.655 | 1.4 | 0.831 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT | IMMUNOGC_C4839 | CD28 | mRNA | 0 |  | Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family | hsa04514;hsa04660;hsa04672;hsa04940;hsa05162;hsa05320;hsa05322;hsa05323;hsa05330;hsa05332;hsa05416 |  | CD28 | NA | azure4 | 1 | -0.213523131672598
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - Signaling by SCF-KIT genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Signalling to p38 via RIT and RIN genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  Rit1-mRNA | 0.201 | 0.343 | -0.472 | 0.874 | 1.15 | 0.721 | 1.83 | 0.56 | 1 | lm.nb | Signalling to p38 via RIT and RIN | IMMUNOGC_C4839 | Rit1 | mRNA | 0 |  | Signalling to p38 via RIT and RIN |  |  | RIT1 | NA | azure4 | 1 | 0.58600583090379
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255

  ##### DE Results - Signalling to p38 via RIT and RIN genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - TNFR2 non-canonical NF-kB pathway genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  TNFRSF4-mRNA | -1.12 | 0.346 | -1.8 | -0.444 | 0.46 | 0.287 | 0.735 | 0.00165 | 0.317 | Wald | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF4 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFRSF4 | NA | slateblue4 | 16 | -3.23699421965318
  TNFRSF17-mRNA | 0.904 | 0.313 | 0.291 | 1.52 | 1.87 | 1.22 | 2.86 | 0.00478 | 0.587 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF17 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04672 | B-cells | TNFRSF17 | NA | azure4 | 1 | 2.88817891373802
  RELB-mRNA | 0.724 | 0.301 | 0.135 | 1.31 | 1.65 | 1.1 | 2.49 | 0.018 | 0.973 | lm.nb | TNFR2 non-canonical NF-kB pathway | IMMUNOGC_C4839 | RELB | mRNA | 0 |  | CLEC7A (Dectin-1) signaling;TNFR2 non-canonical NF-kB pathway | hsa04010;hsa04064;hsa04380;hsa05166;hsa05169 |  | RELB | NA | azure4 | 1 | 2.40531561461794
  Tnfsf4-mRNA | 0.43 | 0.449 | -0.45 | 1.31 | 1.35 | 0.732 | 2.48 | 0.341 | 1 | loglinear | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | Tnfsf4 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFSF4 | NA | azure4 | 1 | 0.957683741648107
  LTA-mRNA | 0.245 | 0.318 | -0.379 | 0.868 | 1.18 | 0.769 | 1.83 | 0.444 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | LTA | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04668;hsa04940;hsa05166;hsa05168 |  | LTA | NA | azure4 | 1 | 0.770440251572327
  CD27-mRNA | 0.181 | 0.263 | -0.334 | 0.696 | 1.13 | 0.793 | 1.62 | 0.493 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | CD27 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | CD27 | NA | azure4 | 1 | 0.688212927756654
  TNFRSF18-mRNA | 0.226 | 0.408 | -0.573 | 1.03 | 1.17 | 0.672 | 2.04 | 0.581 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF18 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFRSF18 | NA | azure4 | 1 | 0.553921568627451
  CD40-mRNA | 0.18 | 0.396 | -0.596 | 0.957 | 1.13 | 0.662 | 1.94 | 0.65 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, TNFR2 non-canonical NF-kB pathway | IMMUNOGC_C4839 | CD40 | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04514;hsa04620;hsa04672;hsa05144;hsa05145;hsa05166;hsa05169;hsa05202;hsa05310;hsa05320;hsa05322;hsa05330;hsa05340;hsa05416 |  | CD40 | NA | azure4 | 1 | 0.454545454545455
  CD40LG-mRNA | -0.0315 | 0.301 | -0.622 | 0.559 | 0.978 | 0.65 | 1.47 | 0.917 | 1 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell, TNFR2 non-canonical NF-kB pathway | IMMUNOGC_C4839 | CD40LG | mRNA | 0 |  | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04514;hsa04660;hsa04672;hsa05144;hsa05145;hsa05310;hsa05320;hsa05322;hsa05330;hsa05340;hsa05416 |  | CD40LG | NA | azure4 | 1 | -0.104651162790698

  ##### DE Results - TNFR2 non-canonical NF-kB pathway genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - TNFs bind their physiological receptors genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  TNFRSF4-mRNA | -1.12 | 0.346 | -1.8 | -0.444 | 0.46 | 0.287 | 0.735 | 0.00165 | 0.317 | Wald | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF4 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFRSF4 | NA | slateblue4 | 16 | -3.23699421965318
  TNFRSF17-mRNA | 0.904 | 0.313 | 0.291 | 1.52 | 1.87 | 1.22 | 2.86 | 0.00478 | 0.587 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF17 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04672 | B-cells | TNFRSF17 | NA | azure4 | 1 | 2.88817891373802
  Tnfsf4-mRNA | 0.43 | 0.449 | -0.45 | 1.31 | 1.35 | 0.732 | 2.48 | 0.341 | 1 | loglinear | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | Tnfsf4 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFSF4 | NA | azure4 | 1 | 0.957683741648107
  LTA-mRNA | 0.245 | 0.318 | -0.379 | 0.868 | 1.18 | 0.769 | 1.83 | 0.444 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | LTA | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060;hsa04064;hsa04668;hsa04940;hsa05166;hsa05168 |  | LTA | NA | azure4 | 1 | 0.770440251572327
  CD27-mRNA | 0.181 | 0.263 | -0.334 | 0.696 | 1.13 | 0.793 | 1.62 | 0.493 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | CD27 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | CD27 | NA | azure4 | 1 | 0.688212927756654
  TNFRSF18-mRNA | 0.226 | 0.408 | -0.573 | 1.03 | 1.17 | 0.672 | 2.04 | 0.581 | 1 | lm.nb | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | IMMUNOGC_C4839 | TNFRSF18 | mRNA | 0 |  | TNFs bind their physiological receptors;TNFR2 non-canonical NF-kB pathway | hsa04060 |  | TNFRSF18 | NA | azure4 | 1 | 0.553921568627451

  ##### DE Results - TNFs bind their physiological receptors genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - Transcriptional regulation of white adipocyte differentiation genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  CEBPB-mRNA | 1.09 | 0.256 | 0.59 | 1.6 | 2.13 | 1.51 | 3.02 | 4.82e-05 | 0.0163 | lm.nb | Senescence-Associated Secretory Phenotype (SASP), Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | CEBPB | mRNA | 0 |  | Transcriptional regulation of white adipocyte differentiation;Senescence-Associated Secretory Phenotype (SASP) | hsa04668;hsa05152;hsa05202 |  | CEBPB | NA | slateblue4 | 16 | 4.2578125
  Klf4-mRNA | 0.599 | 0.272 | 0.0664 | 1.13 | 1.51 | 1.05 | 2.19 | 0.03 | 1 | lm.nb | Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | Klf4 | mRNA | 0 |  | Transcriptional regulation of white adipocyte differentiation | hsa04550 |  | KLF4 | NA | azure4 | 1 | 2.20220588235294
  Egr2-mRNA | 0.574 | 0.342 | -0.0965 | 1.24 | 1.49 | 0.935 | 2.37 | 0.0968 | 1 | lm.nb | Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | Egr2 | mRNA | 0 |  | Transcriptional regulation of white adipocyte differentiation | hsa05161;hsa05166;hsa05203 |  | EGR2 | NA | azure4 | 1 | 1.67836257309941
  TGFB1-mRNA | 0.0846 | 0.418 | -0.735 | 0.905 | 1.06 | 0.601 | 1.87 | 0.84 | 1 | loglinear | Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | TGFB1 | mRNA | 0 |  | ECM proteoglycans;Transcriptional regulation of white adipocyte differentiation | hsa04010;hsa04060;hsa04068;hsa04110;hsa04144;hsa04350;hsa04380;hsa04390;hsa04672;hsa04932;hsa04933;hsa05140;hsa05142;hsa05144;hsa05145;hsa05146;hsa05152;hsa05161;hsa05166;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05220;hsa05321;hsa05323;hsa05410 |  | TGFB1 | NA | azure4 | 1 | 0.202392344497608

  ##### DE Results - Transcriptional regulation of white adipocyte differentiation genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - VEGFA-VEGFR2 Pathway genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  MAPK13-mRNA | 0.881 | 0.334 | 0.226 | 1.54 | 1.84 | 1.17 | 2.9 | 0.00985 | 0.738 | lm.nb | VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | MAPK13 | mRNA | 0 |  | DSCAM interactions;VEGFA-VEGFR2 Pathway | hsa04010;hsa04015;hsa04068;hsa04071;hsa04261;hsa04370;hsa04380;hsa04550;hsa04611;hsa04620;hsa04621;hsa04622;hsa04660;hsa04664;hsa04668;hsa04670;hsa04722;hsa04723;hsa04728;hsa04750;hsa04912;hsa04914;hsa04917;hsa04933;hsa05014;hsa05120;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05164;hsa05169;hsa05205 |  | MAPK13 | NA | azure4 | 1 | 2.6377245508982
  VEGFA-mRNA | 0.725 | 0.301 | 0.136 | 1.31 | 1.65 | 1.1 | 2.49 | 0.0178 | 0.973 | lm.nb | VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | VEGFA | mRNA | 0 |  | EPHA-mediated growth cone collapse;VEGFR2 mediated cell proliferation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04066;hsa04150;hsa04151;hsa04370;hsa04510;hsa04933;hsa05200;hsa05205;hsa05206;hsa05211;hsa05212;hsa05219;hsa05323 |  | VEGFA | NA | azure4 | 1 | 2.40863787375415
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  MAPK11-mRNA | 0.205 | 0.337 | -0.457 | 0.866 | 1.15 | 0.729 | 1.82 | 0.546 | 1 | lm.nb | MyD88.CL.Mal cascade initiated on plasma membrane, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | MAPK11 | mRNA | 0 |  | Activation of the AP-1 family of transcription factors;ERKMAPK targets;VEGFA-VEGFR2 Pathway;activated TAK1 mediates p38 MAPK activation;MyD88.CL.Mal cascade initiated on plasma membrane | hsa04010;hsa04015;hsa04068;hsa04071;hsa04261;hsa04370;hsa04380;hsa04550;hsa04611;hsa04620;hsa04621;hsa04622;hsa04660;hsa04664;hsa04668;hsa04670;hsa04722;hsa04723;hsa04728;hsa04750;hsa04912;hsa04914;hsa04917;hsa04933;hsa05014;hsa05120;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05164;hsa05169;hsa05205 |  | MAPK11 | NA | azure4 | 1 | 0.608308605341246
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255
  AKT3-mRNA | 0.00374 | 0.301 | -0.586 | 0.594 | 1 | 0.666 | 1.51 | 0.99 | 1 | lm.nb | Costimulation by the CD28 family, DAP12 interactions, DAP12 signaling, Downstream signal transduction, Generic Transcription Pathway, GPVI-mediated activation cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, VEGFA-VEGFR2 Pathway | IMMUNOGC_C4839 | AKT3 | mRNA | 0 |  | GPVI-mediated activation cascade;Generic Transcription Pathway;PIP3 activates AKT signaling;Downstream signal transduction;Signaling by SCF-KIT;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;Costimulation by the CD28 family;VEGFA-VEGFR2 Pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04210;hsa04261;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04630;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04728;hsa04910;hsa04914;hsa04915;hsa04917;hsa04920;hsa04931;hsa04932;hsa04933;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05162;hsa05164;hsa05166;hsa05169;hsa05200;hsa05205;hsa05210;hsa05211;hsa05212;hsa05215;hsa05220;hsa05221;hsa05222;hsa05230;hsa05231 |  | AKT3 | NA | azure4 | 1 | 0.0124252491694352

  ##### DE Results - VEGFA-VEGFR2 Pathway genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

- Volcano Plot: Gender_1: 2 vs.1
  More Plot Information

  ##### Volcano Plot: Gender_1: 2 vs.1

  Volcano plot displaying each gene's -log10(p-value) and log2 fold change for the selected covariate. Highly statistically significant genes fall at the top of the plot, and highly differentially expressed genes fall to either side. Genes within the selected gene set are highlighted in orange. Horizontal lines indicate various False Discovery Rate (FDR) thresholds.

- DE Results - VEGFR2 mediated cell proliferation genes - Gender_1: 2 vs.1
  More Plot Information Download CSV Data

  Probe Label | Log2 fold change | std error (log2) | Lower confidence limit (log2) | Upper confidence limit (log2) | Linear fold change | Lower confidence limit (linear) | Upper confidence limit (linear) | P-value | BY.p.value | method | Gene.sets | Codeset.Name | Probe.Label | Analyte.Type | Is.Control | Control.Type | Probe.Annotation | KEGG.Pathways | Cell.Type | Official.Gene.Name | Control.Conc | volcanocol | volcanopch | tstats.all
  IL3RA-mRNA | 0.838 | 0.287 | 0.275 | 1.4 | 1.79 | 1.21 | 2.64 | 0.00441 | 0.587 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640 |  | IL3RA | NA | azure4 | 1 | 2.9198606271777
  VEGFA-mRNA | 0.725 | 0.301 | 0.136 | 1.31 | 1.65 | 1.1 | 2.49 | 0.0178 | 0.973 | lm.nb | VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | VEGFA | mRNA | 0 |  | EPHA-mediated growth cone collapse;VEGFR2 mediated cell proliferation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04066;hsa04150;hsa04151;hsa04370;hsa04510;hsa04933;hsa05200;hsa05205;hsa05206;hsa05211;hsa05212;hsa05219;hsa05323 |  | VEGFA | NA | azure4 | 1 | 2.40863787375415
  IL5RA-mRNA | 0.648 | 0.346 | -0.0292 | 1.33 | 1.57 | 0.98 | 2.51 | 0.0639 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL5RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04630;hsa04640 |  | IL5RA | NA | azure4 | 1 | 1.8728323699422
  NCAM1-mRNA | -0.461 | 0.332 | -1.11 | 0.19 | 0.726 | 0.463 | 1.14 | 0.168 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NCAM1 | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04514;hsa05020 |  | NCAM1 | NA | azure4 | 1 | -1.38855421686747
  NEFL-mRNA | 0.473 | 0.343 | -0.2 | 1.15 | 1.39 | 0.871 | 2.21 | 0.172 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | NEFL | mRNA | 0 |  | RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa05014 |  | NEFL | NA | azure4 | 1 | 1.37900874635569
  KIT-mRNA | 0.495 | 0.39 | -0.27 | 1.26 | 1.41 | 0.83 | 2.39 | 0.208 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAFMAP kinase cascade, Role of LAT2NTALLAB on calcium mobilization, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | KIT | mRNA | 0 |  | RAFMAP kinase cascade;Signaling by SCF-KIT;Downstream signal transduction;Role of LAT2NTALLAB on calcium mobilization;DAP12 signaling;Signaling by PDGF;DAP12 interactions;VEGFR2 mediated cell proliferation;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;VEGFA-VEGFR2 Pathway | hsa04014;hsa04015;hsa04060;hsa04072;hsa04144;hsa04151;hsa04640;hsa05200;hsa05221;hsa05230 |  | KIT | NA | azure4 | 1 | 1.26923076923077
  IL3-mRNA | -0.36 | 0.299 | -0.946 | 0.226 | 0.779 | 0.519 | 1.17 | 0.232 | 1 | Wald | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL3 | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04151;hsa04210;hsa04630;hsa04640;hsa04664;hsa05202;hsa05310 |  | IL3 | NA | azure4 | 1 | -1.20401337792642
  MAP2K1-mRNA | 0.289 | 0.256 | -0.213 | 0.79 | 1.22 | 0.863 | 1.73 | 0.262 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAP2K1 | mRNA | 0 |  | MyD88.CL.Mal cascade initiated on plasma membrane;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions;RAF-independent MAPK13 activation;Negative regulation of MAPK pathway | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04151;hsa04370;hsa04380;hsa04510;hsa04550;hsa04620;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa05020;hsa05161;hsa05164;hsa05200;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAP2K1 | NA | azure4 | 1 | 1.12890625
  MAPK1-mRNA | 0.309 | 0.283 | -0.246 | 0.864 | 1.24 | 0.843 | 1.82 | 0.278 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, MyD88.CL.Mal cascade initiated on plasma membrane, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | MAPK1 | mRNA | 0 |  | Growth hormone receptor signaling;RAF-independent MAPK13 activation;ERKMAPK targets;MyD88.CL.Mal cascade initiated on plasma membrane;FCERI mediated MAPK activation;Negative regulation of MAPK pathway;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010;hsa04012;hsa04014;hsa04015;hsa04024;hsa04062;hsa04066;hsa04068;hsa04071;hsa04072;hsa04150;hsa04151;hsa04261;hsa04350;hsa04370;hsa04380;hsa04510;hsa04550;hsa04611;hsa04620;hsa04621;hsa04650;hsa04660;hsa04662;hsa04664;hsa04668;hsa04722;hsa04723;hsa04910;hsa04912;hsa04914;hsa04915;hsa04917;hsa04921;hsa04933;hsa05010;hsa05020;hsa05131;hsa05132;hsa05133;hsa05140;hsa05142;hsa05145;hsa05152;hsa05160;hsa05161;hsa05164;hsa05200;hsa05203;hsa05205;hsa05206;hsa05210;hsa05211;hsa05212;hsa05215;hsa05219;hsa05220;hsa05221;hsa05230;hsa05231 |  | MAPK1 | NA | azure4 | 1 | 1.09187279151943
  DUSP1-mRNA | 0.361 | 0.399 | -0.42 | 1.14 | 1.28 | 0.748 | 2.21 | 0.367 | 1 | loglinear | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | DUSP1 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP1 | NA | azure4 | 1 | 0.904761904761905
  IL2RA-mRNA | -0.166 | 0.351 | -0.854 | 0.522 | 0.891 | 0.553 | 1.44 | 0.638 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, G beta.CL.gamma signalling through PI3Kgamma, GPVI-mediated activation cascade, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | IL2RA | mRNA | 0 |  | G beta.CL.gamma signalling through PI3Kgamma;RAFMAP kinase cascade;GPVI-mediated activation cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04060;hsa04144;hsa04151;hsa04630;hsa04640;hsa05162;hsa05166 |  | IL2RA | NA | azure4 | 1 | -0.472934472934473
  Dusp5-mRNA | 0.0784 | 0.357 | -0.622 | 0.779 | 1.06 | 0.65 | 1.72 | 0.827 | 1 | lm.nb | DAP12 interactions, DAP12 signaling, Downstream signal transduction, FCERI mediated MAPK activation, RAF-independent MAPK13 activation, RAFMAP kinase cascade, Signaling by PDGF, Signaling by SCF-KIT, Signalling to p38 via RIT and RIN, VEGFA-VEGFR2 Pathway, VEGFR2 mediated cell proliferation | IMMUNOGC_C4839 | Dusp5 | mRNA | 0 |  | RAF-independent MAPK13 activation;RAFMAP kinase cascade;Downstream signal transduction;VEGFR2 mediated cell proliferation;Signaling by SCF-KIT;Signalling to p38 via RIT and RIN;FCERI mediated MAPK activation;DAP12 signaling;Signaling by PDGF;VEGFA-VEGFR2 Pathway;DAP12 interactions | hsa04010 |  | DUSP5 | NA | azure4 | 1 | 0.219607843137255

  ##### DE Results - VEGFR2 mediated cell proliferation genes - Gender_1: 2 vs.1

  Table displaying each sample's global significance scores and directed global significance scores as defined in the heatmaps above. The global significance score is calculated as the square root of the mean squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis. The directed global significance score is calculated as the square root of the mean signed squared t-statistic for the genes in a gene set, with t-statistics coming from the linear regression underlying our differential expression analysis.

Pathview is used to overlay differential expression results on KEGG pathways

Gender_1:
- Gender_1: differential expression in 2 vs. baseline of 1

Pathways:

- Hematopoietic cell lineage
- Cytokine-cytokine receptor interaction
- HTLV-I infection
- Tuberculosis
- TNF signaling pathway
- Hepatitis B
- Inflammatory bowel disease (IBD)
- Chagas disease (American trypanosomiasis)
- T cell receptor signaling pathway
- Toll-like receptor signaling pathway
- Influenza A
- Toxoplasmosis
- PI3K-Akt signaling pathway
- MAPK signaling pathway
- Leishmaniasis
- Osteoclast differentiation
- Jak-STAT signaling pathway
- Pathways in cancer
- Chemokine signaling pathway
- Measles

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

- More Plot Information

  #####

  For each KEGG pathway, genes within the panel are mapped to the pathway and differential expression information is overlaid on the protein-based KEGG pathway image. Pathway nodes shown in white have no genes in the panel that map to them. Pathway nodes in grey have corresponding genes in the panel, however no significant differential expression is observed. Nodes in blue denote downregulation relative to the selected baseline, whereas nodes in orange denote upregulation relative to the selected baseline.

Genes previously shown to be characteristic of various cell populations are used to measure these populations' abundance. QC plots explore the validity of each cell type's measurements, Summary plots explore the joint behavior of cell types, and Covariates plots compare cell type measurements to covariates. In addition to raw cell type abundance measurements, relative abundances measuring various contrasts between cell types are reported.

- QC
- Summary
- Covariates

- QC

- Raw
- Relative

- Raw
- Relative

Choose a Cell Type:

- Summary
- B-cells
- CD8 T cells
- Cytotoxic cells
- DC
- Macrophages
- Mast cells
- Neutrophils
- NK CD56dim cells
- NK cells
- T-cells
- Th1 cells
- Treg

- Barplot of p-values across cell types
  More Plot Information

  ##### Barplot of p-values across cell types

  Barplot of p-values across cell types. p-values are -log10 transformed. Bars above the solid black line indicate statistically significant cell types at an alpha level of 0.01. Bars above the dashed black line indicate statistically significant cell types at an alpha level of 0.001.

- QC Plot for Cell Type Measurements: B-cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: B-cells

  Normalized expression of the genes characteristic of B-cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: CD8 T cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: CD8 T cells

  Normalized expression of the genes characteristic of CD8 T cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Cytotoxic cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Cytotoxic cells

  Normalized expression of the genes characteristic of Cytotoxic cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: DC
  More Plot Information

  ##### QC Plot for Cell Type Measurements: DC

  Normalized expression of the genes characteristic of DC. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Macrophages
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Macrophages

  Normalized expression of the genes characteristic of Macrophages. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Mast cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Mast cells

  Normalized expression of the genes characteristic of Mast cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Neutrophils
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Neutrophils

  Normalized expression of the genes characteristic of Neutrophils. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: NK CD56dim cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: NK CD56dim cells

  Normalized expression of the genes characteristic of NK CD56dim cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: NK cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: NK cells

  Normalized expression of the genes characteristic of NK cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: T-cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: T-cells

  Normalized expression of the genes characteristic of T-cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Th1 cells
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Th1 cells

  Normalized expression of the genes characteristic of Th1 cells. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

- QC Plot for Cell Type Measurements: Treg
  More Plot Information

  ##### QC Plot for Cell Type Measurements: Treg

  Normalized expression of the genes characteristic of Treg. If a cell type's characteristic genes are specific to the cell type and stably expressed within it, they will be strongly correlated with a slope of 1. Substantial departures from this pattern indicate noisier quantification of cell type abundance.

Choose a Cell Type:

- Summary
- T-cells
- DC
- NK cells
- B-cells
- NK CD56dim cells
- Cytotoxic cells
- CD8 T cells
- Macrophages
- Mast cells
- Th1 cells
- Neutrophils
- Treg

- Heatmap of Raw cell type measurements
  More Plot Information Download raw cell type measurements

  ##### Heatmap of Raw cell type measurements

  Heatmap showing raw abundance of cell types. Orange indicates high abundance; blue indicates low abundance. Note that our methods do not support the conclusion that one cell type is more abundant than another. Rather, they support the claim that a given cell type is more abundant in one sample than in another.

- Heatmap of Correlation Matrix of Raw cell type measurements
  More Plot Information

  ##### Heatmap of Correlation Matrix of Raw cell type measurements

  Heatmap showing the correlation matrix of raw cell abundance. Orange and blue indicate positive and negative correlation, respectively.

- T-cells measurements vs. other cell type measurements
  More Plot Information

  ##### T-cells measurements vs. other cell type measurements

  Each panel plots T-cells against another raw abundance measurements. Points are colored by Gender_1.

- DC measurements vs. other cell type measurements
  More Plot Information

  ##### DC measurements vs. other cell type measurements

  Each panel plots DC against another raw abundance measurements. Points are colored by Gender_1.

- NK cells measurements vs. other cell type measurements
  More Plot Information

  ##### NK cells measurements vs. other cell type measurements

  Each panel plots NK cells against another raw abundance measurements. Points are colored by Gender_1.

- B-cells measurements vs. other cell type measurements
  More Plot Information

  ##### B-cells measurements vs. other cell type measurements

  Each panel plots B-cells against another raw abundance measurements. Points are colored by Gender_1.

- NK CD56dim cells measurements vs. other cell type measurements
  More Plot Information

  ##### NK CD56dim cells measurements vs. other cell type measurements

  Each panel plots NK CD56dim cells against another raw abundance measurements. Points are colored by Gender_1.

- Cytotoxic cells measurements vs. other cell type measurements
  More Plot Information

  ##### Cytotoxic cells measurements vs. other cell type measurements

  Each panel plots Cytotoxic cells against another raw abundance measurements. Points are colored by Gender_1.

- CD8 T cells measurements vs. other cell type measurements
  More Plot Information

  ##### CD8 T cells measurements vs. other cell type measurements

  Each panel plots CD8 T cells against another raw abundance measurements. Points are colored by Gender_1.

- Macrophages measurements vs. other cell type measurements
  More Plot Information

  ##### Macrophages measurements vs. other cell type measurements

  Each panel plots Macrophages against another raw abundance measurements. Points are colored by Gender_1.

- Mast cells measurements vs. other cell type measurements
  More Plot Information

  ##### Mast cells measurements vs. other cell type measurements

  Each panel plots Mast cells against another raw abundance measurements. Points are colored by Gender_1.

- Th1 cells measurements vs. other cell type measurements
  More Plot Information

  ##### Th1 cells measurements vs. other cell type measurements

  Each panel plots Th1 cells against another raw abundance measurements. Points are colored by Gender_1.

- Neutrophils measurements vs. other cell type measurements
  More Plot Information

  ##### Neutrophils measurements vs. other cell type measurements

  Each panel plots Neutrophils against another raw abundance measurements. Points are colored by Gender_1.

- Treg measurements vs. other cell type measurements
  More Plot Information

  ##### Treg measurements vs. other cell type measurements

  Each panel plots Treg against another raw abundance measurements. Points are colored by Gender_1.

Choose a Cell Type:

- Summary
- CD8.vs..Treg
- CD4.vs..T.cells

- Heatmap of Relative cell type measurements
  More Plot Information Download relative cell type measurements

  ##### Heatmap of Relative cell type measurements

  Heatmap showing relative abundance of cell types. Orange indicates high abundance; blue indicates low abundance. Note that our methods do not support the conclusion that one cell type is more abundant than another. Rather, they support the claim that a given cell type is more abundant in one sample than in another.

- Heatmap of Correlation Matrix of Relative cell type measurements
  More Plot Information

  ##### Heatmap of Correlation Matrix of Relative cell type measurements

  Heatmap showing the correlation matrix of relative cell abundance. Orange and blue indicate positive and negative correlation, respectively.

- CD8.vs..Treg measurements vs. other cell type measurements
  More Plot Information

  ##### CD8.vs..Treg measurements vs. other cell type measurements

  Each panel plots CD8.vs..Treg against another relative abundance measurements. Points are colored by Gender_1.

- CD4.vs..T.cells measurements vs. other cell type measurements
  More Plot Information

  ##### CD4.vs..T.cells measurements vs. other cell type measurements

  Each panel plots CD4.vs..T.cells against another relative abundance measurements. Points are colored by Gender_1.

Choose a Cell Type:

- Summary
- T-cells
- DC
- NK cells
- B-cells
- NK CD56dim cells
- Cytotoxic cells
- CD8 T cells
- Macrophages
- Mast cells
- Th1 cells
- Neutrophils
- Treg

- Raw cell type measurements vs. Gender_1
  More Plot Information

  ##### Raw cell type measurements vs. Gender_1

  Plots the raw cell type abundance measurements against Gender_1.

- T-cells Measurement vs. Gender_1
  More Plot Information

  ##### T-cells Measurement vs. Gender_1

  Plots T-cells measurements against Gender_1.

- DC Measurement vs. Gender_1
  More Plot Information

  ##### DC Measurement vs. Gender_1

  Plots DC measurements against Gender_1.

- NK cells Measurement vs. Gender_1
  More Plot Information

  ##### NK cells Measurement vs. Gender_1

  Plots NK cells measurements against Gender_1.

- B-cells Measurement vs. Gender_1
  More Plot Information

  ##### B-cells Measurement vs. Gender_1

  Plots B-cells measurements against Gender_1.

- NK CD56dim cells Measurement vs. Gender_1
  More Plot Information

  ##### NK CD56dim cells Measurement vs. Gender_1

  Plots NK CD56dim cells measurements against Gender_1.

- Cytotoxic cells Measurement vs. Gender_1
  More Plot Information

  ##### Cytotoxic cells Measurement vs. Gender_1

  Plots Cytotoxic cells measurements against Gender_1.

- CD8 T cells Measurement vs. Gender_1
  More Plot Information

  ##### CD8 T cells Measurement vs. Gender_1

  Plots CD8 T cells measurements against Gender_1.

- Macrophages Measurement vs. Gender_1
  More Plot Information

  ##### Macrophages Measurement vs. Gender_1

  Plots Macrophages measurements against Gender_1.

- Mast cells Measurement vs. Gender_1
  More Plot Information

  ##### Mast cells Measurement vs. Gender_1

  Plots Mast cells measurements against Gender_1.

- Th1 cells Measurement vs. Gender_1
  More Plot Information

  ##### Th1 cells Measurement vs. Gender_1

  Plots Th1 cells measurements against Gender_1.

- Neutrophils Measurement vs. Gender_1
  More Plot Information

  ##### Neutrophils Measurement vs. Gender_1

  Plots Neutrophils measurements against Gender_1.

- Treg Measurement vs. Gender_1
  More Plot Information

  ##### Treg Measurement vs. Gender_1

  Plots Treg measurements against Gender_1.

Choose a Cell Type:

- Summary
- CD8.vs..Treg
- CD4.vs..T.cells

- Relative cell type measurements vs. Gender_1
  More Plot Information

  ##### Relative cell type measurements vs. Gender_1

  Plots the relative cell type abundance measurements against Gender_1.

- CD8.vs..Treg Measurement vs. Gender_1
  More Plot Information

  ##### CD8.vs..Treg Measurement vs. Gender_1

  Plots CD8.vs..Treg measurements against Gender_1.

- CD4.vs..T.cells Measurement vs. Gender_1
  More Plot Information

  ##### CD4.vs..T.cells Measurement vs. Gender_1

  Plots CD4.vs..T.cells measurements against Gender_1.

Summary of the options that were chosen when running this analysis.

##### Analysis Details

Analysis name: New Analysis 22
Location of results: C:\Users\Jeff\Desktop\nSolver
File type of plots: png

##### Sample Annotation Details

Unique sample identifier: File.Name
Covariate1: Gender_1; Variable Type: categorical; Reference Level: 1

##### Gene Annotation Details

Column defining probe set membership: Probe.Annotation
Probe annotation column giving cell type-specific probes: Cell.Type

##### Fusion Analysis Details

Perform fusion analysis: No
p-value end probe threshold: 0.05
p-value junction probe threshold: 0.05

##### SNV Analysis Details

Perform snv analysis: No
Fold change threshold(s): 1, 2
p-value threshold(s): 0.01, 0.01
Reference samples:
NA
Use EM post processing: Yes
Use debiasing post processing: Yes

##### Normalization Details

Perform normalization on: mRNA
Number of normalization probes: mRNA: 10

##### Pathway Scoring Analysis Details

Perform pathway scoring analysis: TRUE
Covariates to include in plots: Gender_1

##### Differential Expression Analysis Details

Perform differential expression testing: TRUE
Predictors: Gender_1
Confounders: none
P-value adjustment: BY
Run gene set analysis TRUE

##### Pathview Details

Display results using Pathview: TRUE
Color Pathview pathview plots by: Fold-change
P-value threshold: 0.05
Additional KEGG IDs: none

##### Cell Type Profiling Details

Perform cell type profiling: TRUE
Covariates to include in plots: Gender_1
Use all cell type genes or dynamically select a subset:
P-value threshold for reporting a cell type's results: 1
Show results at the level of raw cell type abundance: TRUE
Show results at the level of relative cell type abundance: TRUE
Use default contrasts for calculating relative cell type abundance: TRUE

##### Probe Descriptive Analysis Details

Run Probe Descriptive analysis: FALSE

##### Related Analytes Analysis Details

Related Analytes Analysis: FALSE

##### Warnings

Warning: the following probe sets hold less than 5 probes and will be discarded: activated TAK1 mediates p38 MAPK activation, Activation of BMF and translocation to mitochondria, Activation of IRF3IRF7 mediated by TBK1IKK epsilon, Activation of the AP-1 family of transcription factors, Binding and entry of HIV virion, CD209 (DC-SIGN) signaling, CLEC7A (Dectin-1) signaling, Downstream TCR signaling, DSCAM interactions, ECM proteoglycans, EPHA-mediated growth cone collapse, ERKMAPK targets, FCERI mediated Ca.PLS.2 mobilization, FCGR activation, Formyl peptide receptors bind formyl peptides and many other ligands, Growth hormone receptor signaling, Interferon alphabeta signaling, JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1, MyD88 deficiency (TLR24), Nef Mediated CD4 Down-regulation, Negative regulation of MAPK pathway, NOD12 Signaling Pathway, O-glycosylation of TSR domain-containing proteins, Oxidative Stress Induced Senescence, p38MAPK events, PD-1 signaling, Phosphorylation of CD3 and TCR zeta chains, PIP3 activates AKT signaling, Platelet degranulation , Pre-NOTCH Transcription and Translation, Regulation of actin dynamics for phagocytic cup formation, Regulation of TNFR1 signaling, RIP-mediated NFkB activation via ZBP1, RNA Polymerase II Transcription Initiation, Small interfering RNA (siRNA) biogenesis, TAK1 activates NFkB by phosphorylation and activation of IKKs complex, TNFR1-mediated ceramide production, TRAF6 mediated NF-kB activation
Warning: the following cell types in the cell types contrast file were not found in the probe annotation file's cell type column:
CD45, Exhausted CD8
Therefore the following contrasts have been discarded:
Total.TILs
B.cells.vs..TILs
Cytotoxic.cells.vs..TILs
DC.vs..TILs
Exhausted.CD8.vs..TILs
Macrophages.vs..TILs
Mast.cells.vs..TILs
Neutrophils.vs..TILs
NK.CD56dim.cells.vs..TILs
NK.cells.vs..TILs
T.cells.vs..TILs
Th1.cells.vs..TILs
Treg.vs..TILs
CD8.T.cells.vs..TILs
CD8.vs..Exhasuted.CD8
Degradation of the extracellular matrix, G beta.CL.gamma signalling through PI3Kgamma, Interleukin-1 signaling, MicroRNA (miRNA) biogenesis, Role of LAT2NTALLAB on calcium mobilization, Senescence-Associated Secretory Phenotype (SASP), Transcriptional regulation of white adipocyte differentiation pathways dropped from Pathway Scoring Analysis due to low number of probes.