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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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

- BMI

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

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. BMI
  More Plot Information

  ##### Pathway scores vs. BMI

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

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

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

  Plots Chemokine receptors bind chemokines pathway scores against BMI.

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

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

  Plots Costimulation by the CD28 family pathway scores against BMI.

- DAP12 interactions pathway scores vs. BMI
  More Plot Information

  ##### DAP12 interactions pathway scores vs. BMI

  Plots DAP12 interactions pathway scores against BMI.

- DAP12 signaling pathway scores vs. BMI
  More Plot Information

  ##### DAP12 signaling pathway scores vs. BMI

  Plots DAP12 signaling pathway scores against BMI.

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

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

  Plots Downstream signal transduction pathway scores against BMI.

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

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

  Plots FCERI mediated MAPK activation pathway scores against BMI.

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

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

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

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

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

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

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

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

  Plots Generic Transcription Pathway pathway scores against BMI.

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

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

  Plots GPVI-mediated activation cascade pathway scores against BMI.

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

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

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

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

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

  Plots Metabolism of carbohydrates pathway scores against BMI.

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

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

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

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

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

  Plots Peptide ligand-binding receptors pathway scores against BMI.

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

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

  Plots RAF-independent MAPK13 activation pathway scores against BMI.

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

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

  Plots RAFMAP kinase cascade pathway scores against BMI.

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

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

  Plots Signaling by PDGF pathway scores against BMI.

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

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

  Plots Signaling by SCF-KIT pathway scores against BMI.

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

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

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

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

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

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

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

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

  Plots TNFs bind their physiological receptors pathway scores against BMI.

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

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

  Plots VEGFA-VEGFR2 Pathway pathway scores against BMI.

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

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

  Plots VEGFR2 mediated cell proliferation pathway scores against BMI.

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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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: BMI
  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
  TGFB2-mRNA | 0.206 | 0.0204 | 0.166 | 0.246 | 1.15 | 1.12 | 1.19 | 1.42e-16 | 1.92e-13 | Wald |  | NM_003238.2:1125
  SAAS-mRNA | 0.141 | 0.0183 | 0.105 | 0.177 | 1.1 | 1.08 | 1.13 | 1.42e-11 | 9.6e-09 | Wald |  | NM_013271.2:570
  IL6-mRNA | 0.148 | 0.022 | 0.105 | 0.192 | 1.11 | 1.08 | 1.14 | 1.32e-09 | 5.95e-07 | Wald | RAF-independent MAPK13 activation, Senescence-Associated Secretory Phenotype (SASP) | NM_000600.3:364
  CD9-mRNA | 0.216 | 0.0338 | 0.15 | 0.282 | 1.16 | 1.11 | 1.22 | 6.58e-09 | 2.22e-06 | lm.nb |  | NM_001769.2:405
  LTK-mRNA | 0.127 | 0.0209 | 0.0857 | 0.168 | 1.09 | 1.06 | 1.12 | 2.95e-08 | 7.96e-06 | Wald |  | NM_002344.5:564
  F13A1-mRNA | 0.177 | 0.0337 | 0.111 | 0.244 | 1.13 | 1.08 | 1.18 | 9.1e-07 | 0.000205 | lm.nb |  | NM_000129.3:3196
  Il1rn-mRNA | -0.158 | 0.0335 | -0.223 | -0.092 | 0.897 | 0.857 | 0.938 | 8.59e-06 | 0.00146 | lm.nb | Interleukin-1 signaling | NM_000577.3:480
  ADAM9-mRNA | 0.121 | 0.0256 | 0.0704 | 0.171 | 1.09 | 1.05 | 1.13 | 8.65e-06 | 0.00146 | lm.nb | Degradation of the extracellular matrix | NM_001005845.1:695
  TNFRSF4-mRNA | 0.116 | 0.0282 | 0.061 | 0.171 | 1.08 | 1.04 | 1.13 | 8.14e-05 | 0.011 | Wald | TNFR2 non-canonical NF-kB pathway, TNFs bind their physiological receptors | NM_003327.3:981
  RAB11A-mRNA | 0.13 | 0.0316 | 0.0683 | 0.192 | 1.09 | 1.05 | 1.14 | 8.17e-05 | 0.011 | lm.nb |  | NM_004663.3:710
  Areg-mRNA | 0.0964 | 0.025 | 0.0474 | 0.145 | 1.07 | 1.03 | 1.11 | 0.00021 | 0.0257 | Wald |  | NM_001657.2:547
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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_000417.1:1000
  Rit1-mRNA | 0.0959 | 0.0265 | 0.044 | 0.148 | 1.07 | 1.03 | 1.11 | 0.000473 | 0.0491 | lm.nb | Signalling to p38 via RIT and RIN | NM_006912.4:1745
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | NM_005465.4:287
  LYZ-mRNA | -0.0888 | 0.0262 | -0.14 | -0.0374 | 0.94 | 0.907 | 0.974 | 0.00104 | 0.0894 | lm.nb |  | NM_000239.2:305
  CD33-mRNA | -0.0729 | 0.0216 | -0.115 | -0.0306 | 0.951 | 0.923 | 0.979 | 0.00106 | 0.0894 | lm.nb | Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | NM_001177608.1:730
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | NM_000222.1:5
  NFATC4-mRNA | -0.116 | 0.0363 | -0.188 | -0.0453 | 0.922 | 0.878 | 0.969 | 0.00184 | 0.138 | Wald |  | NM_001136022.2:2296
  GADD45A-mRNA | 0.0964 | 0.0314 | 0.0348 | 0.158 | 1.07 | 1.02 | 1.12 | 0.00282 | 0.2 | lm.nb |  | NM_001924.2:865
  SMAD2-mRNA | 0.0693 | 0.023 | 0.0243 | 0.114 | 1.05 | 1.02 | 1.08 | 0.00328 | 0.221 | lm.nb | Generic Transcription Pathway | NM_005901.5:1678

  ##### DE Results: BMI

  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 BMI | Directed BMI
  Chemokine receptors bind chemokines | 1.746 | 1.204
  Costimulation by the CD28 family | 2.171 | 2.146
  DAP12 interactions | 2.151 | 1.926
  DAP12 signaling | 2.109 | 2.108
  Degradation of the extracellular matrix | 3.101 | 2.931
  Downstream signal transduction | 2.072 | 2.065
  FCERI mediated MAPK activation | 1.988 | 1.986
  G alpha (i) signalling events | 1.613 | 1.231
  G alpha (q) signalling events | 1.48 | 1.33
  G beta.CL.gamma signalling through PI3Kgamma | 1.931 | 1.926
  Generic Transcription Pathway | 2.002 | 2.002
  GPVI-mediated activation cascade | 2.305 | 2.302
  Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell | 1.683 | -0.302
  Interleukin-1 signaling | 2.329 | -1.959
  Metabolism of carbohydrates | 1.095 | 1.095
  MicroRNA (miRNA) biogenesis | 1.429 | 1.429
  MyD88.CL.Mal cascade initiated on plasma membrane | 1.687 | 1.656
  Peptide ligand-binding receptors | 1.688 | 1.239
  RAF-independent MAPK13 activation | 3.371 | 3.371
  RAFMAP kinase cascade | 1.983 | 1.981

  ##### 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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  CXCL5-mRNA | 0.103 | 0.0387 | 0.0276 | 0.179 | 1.07 | 1.02 | 1.13 | 0.00884 | 0.411 | 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 | slateblue4 | 16 | 2.66149870801034
  Cxcl10-mRNA | -0.0625 | 0.0276 | -0.117 | -0.00836 | 0.958 | 0.922 | 0.994 | 0.026 | 0.826 | 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 | -2.26449275362319
  CCR5-mRNA | 0.0551 | 0.0244 | 0.00725 | 0.103 | 1.04 | 1.01 | 1.07 | 0.0264 | 0.826 | 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 | 2.25819672131148
  Ccl2-mRNA | 0.0683 | 0.0306 | 0.00826 | 0.128 | 1.05 | 1.01 | 1.09 | 0.0282 | 0.826 | 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 | 2.23202614379085
  CXCR4-mRNA | 0.0595 | 0.0288 | 0.00298 | 0.116 | 1.04 | 1 | 1.08 | 0.0419 | 0.961 | 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 | 2.06597222222222
  Ccl4-mRNA | -0.0613 | 0.032 | -0.124 | 0.00133 | 0.958 | 0.918 | 1 | 0.0581 | 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 | -1.915625
  CXCR6-mRNA | 0.0362 | 0.0249 | -0.0126 | 0.0851 | 1.03 | 0.991 | 1.06 | 0.149 | 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 | 1.45381526104418
  CCR3-mRNA | 0.0256 | 0.0284 | -0.0301 | 0.0812 | 1.02 | 0.979 | 1.06 | 0.37 | 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 | 0.901408450704225
  Ccl3-mRNA | 0.0186 | 0.0352 | -0.0504 | 0.0875 | 1.01 | 0.966 | 1.06 | 0.599 | 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 | 0.528409090909091
  CXCL8-mRNA | 0.017 | 0.0522 | -0.0854 | 0.119 | 1.01 | 0.943 | 1.09 | 0.746 | 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 | 0.325670498084291
  CCR2-mRNA | 0.00219 | 0.0205 | -0.0379 | 0.0423 | 1 | 0.974 | 1.03 | 0.915 | 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 | 0.106829268292683

  ##### DE Results - Chemokine receptors bind chemokines genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  CTLA4-mRNA | 0.0833 | 0.028 | 0.0285 | 0.138 | 1.06 | 1.02 | 1.1 | 0.00367 | 0.231 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | CTLA4 | mRNA | 0 |  | Costimulation by the CD28 family | hsa04514;hsa04660;hsa05320;hsa05323 |  | CTLA4 | NA | slateblue4 | 16 | 2.975
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  BTLA-mRNA | 0.0729 | 0.0272 | 0.0196 | 0.126 | 1.05 | 1.01 | 1.09 | 0.00864 | 0.411 | lm.nb | Costimulation by the CD28 family | IMMUNOGC_C4839 | BTLA | mRNA | 0 |  | Costimulation by the CD28 family |  |  | BTLA | NA | slateblue4 | 16 | 2.68014705882353
  ICOS-mRNA | 0.0597 | 0.0232 | 0.0143 | 0.105 | 1.04 | 1.01 | 1.08 | 0.0115 | 0.485 | 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 | 2.57327586206897
  CD3G-mRNA | 0.0418 | 0.0244 | -0.00605 | 0.0896 | 1.03 | 0.996 | 1.06 | 0.0902 | 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 | 1.71311475409836
  CD3E-mRNA | 0.0292 | 0.0238 | -0.0175 | 0.076 | 1.02 | 0.988 | 1.05 | 0.223 | 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 | 1.22689075630252
  PDCD1-mRNA | 0.0232 | 0.0305 | -0.0366 | 0.083 | 1.02 | 0.975 | 1.06 | 0.449 | 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 | 0.760655737704918
  CD274-mRNA | -0.0206 | 0.0282 | -0.0759 | 0.0346 | 0.986 | 0.949 | 1.02 | 0.466 | 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 | -0.730496453900709
  CD4-mRNA | 0.00457 | 0.0222 | -0.0389 | 0.0481 | 1 | 0.973 | 1.03 | 0.837 | 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 | 0.205855855855856

  ##### DE Results - Costimulation by the CD28 family genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  Cd300lb-mRNA | -0.0592 | 0.0219 | -0.102 | -0.0163 | 0.96 | 0.932 | 0.989 | 0.00808 | 0.411 | 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 | slateblue4 | 16 | -2.70319634703196
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  KLRD1-mRNA | 0.0323 | 0.0204 | -0.00772 | 0.0724 | 1.02 | 0.995 | 1.05 | 0.117 | 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 | 1.58333333333333
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - DAP12 interactions genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  KLRD1-mRNA | 0.0323 | 0.0204 | -0.00772 | 0.0724 | 1.02 | 0.995 | 1.05 | 0.117 | 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 | 1.58333333333333
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - DAP12 signaling genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | 0.121 | 0.0256 | 0.0704 | 0.171 | 1.09 | 1.05 | 1.13 | 8.65e-06 | 0.00146 | lm.nb | Degradation of the extracellular matrix | IMMUNOGC_C4839 | ADAM9 | mRNA | 0 |  | Degradation of the extracellular matrix |  |  | ADAM9 | NA | slateblue2 | 16 | 4.7265625
  TPSAB1-mRNA | 0.0575 | 0.0258 | 0.00695 | 0.108 | 1.04 | 1 | 1.08 | 0.0282 | 0.826 | Wald | Degradation of the extracellular matrix | IMMUNOGC_C4839 | TPSAB1 | mRNA | 0 |  | Degradation of the extracellular matrix |  | Mast cells | TPSAB1 | NA | azure4 | 1 | 2.22868217054264
  CTSG-mRNA | -0.0285 | 0.023 | -0.0735 | 0.0166 | 0.98 | 0.95 | 1.01 | 0.218 | 1 | Wald | Degradation of the extracellular matrix | IMMUNOGC_C4839 | CTSG | mRNA | 0 |  | Degradation of the extracellular matrix | hsa04080;hsa05146;hsa05322 |  | CTSG | NA | azure4 | 1 | -1.23913043478261

  ##### DE Results - Degradation of the extracellular matrix genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  STAT6-mRNA | -0.0147 | 0.0335 | -0.0804 | 0.0509 | 0.99 | 0.946 | 1.04 | 0.661 | 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 | -0.438805970149254
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - Downstream signal transduction genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  JUN-mRNA | 0.058 | 0.0284 | 0.00236 | 0.114 | 1.04 | 1 | 1.08 | 0.0438 | 0.961 | 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 | 2.04225352112676
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - FCERI mediated MAPK activation genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  CXCL5-mRNA | 0.103 | 0.0387 | 0.0276 | 0.179 | 1.07 | 1.02 | 1.13 | 0.00884 | 0.411 | 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 | slateblue4 | 16 | 2.66149870801034
  Cxcl10-mRNA | -0.0625 | 0.0276 | -0.117 | -0.00836 | 0.958 | 0.922 | 0.994 | 0.026 | 0.826 | 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 | -2.26449275362319
  CCR5-mRNA | 0.0551 | 0.0244 | 0.00725 | 0.103 | 1.04 | 1.01 | 1.07 | 0.0264 | 0.826 | 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 | 2.25819672131148
  CXCR4-mRNA | 0.0595 | 0.0288 | 0.00298 | 0.116 | 1.04 | 1 | 1.08 | 0.0419 | 0.961 | 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 | 2.06597222222222
  PMCH-mRNA | 0.0422 | 0.023 | -0.00282 | 0.0873 | 1.03 | 0.998 | 1.06 | 0.0694 | 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 | 1.83478260869565
  NMUR1-mRNA | 0.0412 | 0.0252 | -0.00819 | 0.0905 | 1.03 | 0.994 | 1.06 | 0.105 | 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 | 1.63492063492063
  CXCR6-mRNA | 0.0362 | 0.0249 | -0.0126 | 0.0851 | 1.03 | 0.991 | 1.06 | 0.149 | 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 | 1.45381526104418
  PTGDR2-mRNA | 0.0285 | 0.0257 | -0.022 | 0.0789 | 1.02 | 0.985 | 1.06 | 0.271 | 1 | lm.nb | G alpha (i) signalling events | IMMUNOGC_C4839 | PTGDR2 | mRNA | 0 |  | G alpha (i) signalling events |  |  | PTGDR2 | NA | azure4 | 1 | 1.10894941634241
  FPR2-mRNA | -0.0284 | 0.0277 | -0.0826 | 0.0259 | 0.981 | 0.944 | 1.02 | 0.308 | 1 | 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 | azure4 | 1 | -1.02527075812274
  TAS2R38-mRNA | -0.028 | 0.0297 | -0.0863 | 0.0303 | 0.981 | 0.942 | 1.02 | 0.348 | 1 | Wald | G alpha (i) signalling events | IMMUNOGC_C4839 | TAS2R38 | mRNA | 0 |  | G alpha (i) signalling events |  |  | TAS2R38 | NA | azure4 | 1 | -0.942760942760943
  CCR3-mRNA | 0.0256 | 0.0284 | -0.0301 | 0.0812 | 1.02 | 0.979 | 1.06 | 0.37 | 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 | 0.901408450704225
  CXCL8-mRNA | 0.017 | 0.0522 | -0.0854 | 0.119 | 1.01 | 0.943 | 1.09 | 0.746 | 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 | 0.325670498084291
  CCR2-mRNA | 0.00219 | 0.0205 | -0.0379 | 0.0423 | 1 | 0.974 | 1.03 | 0.915 | 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 | 0.106829268292683

  ##### DE Results - G alpha (i) signalling events genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  PMCH-mRNA | 0.0422 | 0.023 | -0.00282 | 0.0873 | 1.03 | 0.998 | 1.06 | 0.0694 | 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 | 1.83478260869565
  NMUR1-mRNA | 0.0412 | 0.0252 | -0.00819 | 0.0905 | 1.03 | 0.994 | 1.06 | 0.105 | 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 | 1.63492063492063
  ANXA1-mRNA | 0.0293 | 0.0203 | -0.0104 | 0.069 | 1.02 | 0.993 | 1.05 | 0.151 | 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 | 1.44334975369458
  TRIO-mRNA | 0.0324 | 0.0243 | -0.0153 | 0.0801 | 1.02 | 0.989 | 1.06 | 0.186 | 1 | lm.nb | G alpha (q) signalling events | IMMUNOGC_C4839 | TRIO | mRNA | 0 |  | G alpha (q) signalling events |  |  | TRIO | NA | azure4 | 1 | 1.33333333333333
  FPR2-mRNA | -0.0284 | 0.0277 | -0.0826 | 0.0259 | 0.981 | 0.944 | 1.02 | 0.308 | 1 | 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 | azure4 | 1 | -1.02527075812274

  ##### DE Results - G alpha (q) signalling events genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667

  ##### DE Results - G beta.CL.gamma signalling through PI3Kgamma genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  SMAD2-mRNA | 0.0693 | 0.023 | 0.0243 | 0.114 | 1.05 | 1.02 | 1.08 | 0.00328 | 0.221 | 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 | slateblue4 | 16 | 3.01304347826087
  PRKAA1-mRNA | 0.0516 | 0.0214 | 0.00961 | 0.0936 | 1.04 | 1.01 | 1.07 | 0.018 | 0.666 | 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 | 2.41121495327103
  NR3C1-mRNA | 0.0337 | 0.0208 | -0.00709 | 0.0745 | 1.02 | 0.995 | 1.05 | 0.109 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | NR3C1 | mRNA | 0 |  | Generic Transcription Pathway | hsa04080 |  | NR3C1 | NA | azure4 | 1 | 1.62019230769231
  Ddit4-mRNA | 0.0368 | 0.0283 | -0.0187 | 0.0922 | 1.03 | 0.987 | 1.07 | 0.197 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | Ddit4 | mRNA | 0 |  | Generic Transcription Pathway | hsa04150;hsa04151;hsa05206 |  | DDIT4 | NA | azure4 | 1 | 1.30035335689046
  RORC-mRNA | 0.0258 | 0.0272 | -0.0274 | 0.0791 | 1.02 | 0.981 | 1.06 | 0.344 | 1 | lm.nb | Generic Transcription Pathway | IMMUNOGC_C4839 | RORC | mRNA | 0 |  | Generic Transcription Pathway | hsa05321 |  | RORC | NA | azure4 | 1 | 0.948529411764706
  Junb-mRNA | 0.0201 | 0.0363 | -0.0511 | 0.0914 | 1.01 | 0.965 | 1.07 | 0.581 | 1 | loglinear | Generic Transcription Pathway | IMMUNOGC_C4839 | Junb | mRNA | 0 |  | Generic Transcription Pathway | hsa04380;hsa04668 |  | JUNB | NA | azure4 | 1 | 0.553719008264463
  G6PD-mRNA | -0.00084 | 0.0313 | -0.0621 | 0.0605 | 0.999 | 0.958 | 1.04 | 0.979 | 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 | -0.0268370607028754

  ##### DE Results - Generic Transcription Pathway genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667

  ##### DE Results - GPVI-mediated activation cascade genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  CD33-mRNA | -0.0729 | 0.0216 | -0.115 | -0.0306 | 0.951 | 0.923 | 0.979 | 0.00106 | 0.0894 | 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 | slateblue4 | 16 | -3.375
  Cd300lb-mRNA | -0.0592 | 0.0219 | -0.102 | -0.0163 | 0.96 | 0.932 | 0.989 | 0.00808 | 0.411 | 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 | slateblue4 | 16 | -2.70319634703196
  CD40LG-mRNA | 0.053 | 0.0237 | 0.00657 | 0.0995 | 1.04 | 1 | 1.07 | 0.0276 | 0.826 | 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 | 2.23628691983122
  CD160-mRNA | 0.0358 | 0.0195 | -0.00241 | 0.074 | 1.03 | 0.998 | 1.05 | 0.0695 | 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 | 1.83589743589744
  KLRF1-mRNA | 0.0333 | 0.0207 | -0.00734 | 0.0739 | 1.02 | 0.995 | 1.05 | 0.112 | 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 | 1.60869565217391
  KLRD1-mRNA | 0.0323 | 0.0204 | -0.00772 | 0.0724 | 1.02 | 0.995 | 1.05 | 0.117 | 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 | 1.58333333333333
  NCR1-mRNA | 0.0349 | 0.0255 | -0.0151 | 0.085 | 1.02 | 0.99 | 1.06 | 0.175 | 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 | 1.36862745098039
  LAIR2-mRNA | -0.0371 | 0.0286 | -0.0932 | 0.019 | 0.975 | 0.937 | 1.01 | 0.198 | 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 | -1.2972027972028
  CD3E-mRNA | 0.0292 | 0.0238 | -0.0175 | 0.076 | 1.02 | 0.988 | 1.05 | 0.223 | 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 | 1.22689075630252
  CD40-mRNA | 0.0346 | 0.0319 | -0.028 | 0.0971 | 1.02 | 0.981 | 1.07 | 0.281 | 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 | 1.0846394984326
  KIR3DL1-mRNA | 0.0292 | 0.029 | -0.0277 | 0.0862 | 1.02 | 0.981 | 1.06 | 0.317 | 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 | 1.00689655172414
  CD8B-mRNA | 0.0107 | 0.0273 | -0.0428 | 0.0641 | 1.01 | 0.971 | 1.05 | 0.697 | 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 | 0.391941391941392
  CD62L-mRNA | -0.00825 | 0.0288 | -0.0646 | 0.0481 | 0.994 | 0.956 | 1.03 | 0.775 | 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 | -0.286458333333333
  CD8A-mRNA | -5.83e-05 | 0.0314 | -0.0617 | 0.0615 | 1 | 0.958 | 1.04 | 0.999 | 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 | -0.00185668789808917

  ##### DE Results - Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | -0.158 | 0.0335 | -0.223 | -0.092 | 0.897 | 0.857 | 0.938 | 8.59e-06 | 0.00146 | lm.nb | Interleukin-1 signaling | IMMUNOGC_C4839 | Il1rn | mRNA | 0 |  | Interleukin-1 signaling |  |  | IL1RN | NA | slateblue1 | 16 | -4.71641791044776
  NFKB1-mRNA | 0.0359 | 0.0212 | -0.0056 | 0.0774 | 1.03 | 0.996 | 1.06 | 0.0933 | 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 | 1.69339622641509
  TOLLIP-mRNA | 0.0256 | 0.0244 | -0.0222 | 0.0735 | 1.02 | 0.985 | 1.05 | 0.296 | 1 | lm.nb | Interleukin-1 signaling | IMMUNOGC_C4839 | TOLLIP | mRNA | 0 |  | Interleukin-1 signaling | hsa04620 |  | TOLLIP | NA | azure4 | 1 | 1.04918032786885
  IL1B-mRNA | -0.0281 | 0.0341 | -0.095 | 0.0387 | 0.981 | 0.936 | 1.03 | 0.412 | 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 | -0.824046920821114
  IL1R2-mRNA | -0.0213 | 0.0442 | -0.108 | 0.0653 | 0.985 | 0.928 | 1.05 | 0.631 | 1 | loglinear | Interleukin-1 signaling | IMMUNOGC_C4839 | IL1R2 | mRNA | 0 |  | Interleukin-1 signaling | hsa04010;hsa04060;hsa04640;hsa05146;hsa05166;hsa05202 |  | IL1R2 | NA | azure4 | 1 | -0.481900452488688

  ##### DE Results - Interleukin-1 signaling genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  NUP107-mRNA | 0.048 | 0.0225 | 0.00389 | 0.0921 | 1.03 | 1 | 1.07 | 0.0356 | 0.918 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | NUP107 | mRNA | 0 |  | Metabolism of carbohydrates |  |  | NUP107 | NA | azure4 | 1 | 2.13333333333333
  HPSE-mRNA | 0.0257 | 0.0218 | -0.0171 | 0.0684 | 1.02 | 0.988 | 1.05 | 0.243 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | HPSE | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100;hsa05205 |  | HPSE | NA | azure4 | 1 | 1.17889908256881
  Pfkfb3-mRNA | 0.0309 | 0.0304 | -0.0286 | 0.0905 | 1.02 | 0.98 | 1.06 | 0.311 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | Pfkfb3 | mRNA | 0 |  | Metabolism of carbohydrates | hsa04066 |  | PFKFB3 | NA | azure4 | 1 | 1.01644736842105
  CHIT1-mRNA | 0.0326 | 0.0349 | -0.0359 | 0.101 | 1.02 | 0.975 | 1.07 | 0.353 | 1 | loglinear | Metabolism of carbohydrates | IMMUNOGC_C4839 | CHIT1 | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100 |  | CHIT1 | NA | azure4 | 1 | 0.934097421203438
  GUSB-mRNA | 0.0146 | 0.0244 | -0.0331 | 0.0623 | 1.01 | 0.977 | 1.04 | 0.551 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | GUSB | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100 |  | GUSB | NA | azure4 | 1 | 0.598360655737705
  GAPDH-mRNA | 0.0104 | 0.0238 | -0.0362 | 0.0571 | 1.01 | 0.975 | 1.04 | 0.662 | 1 | lm.nb | Metabolism of carbohydrates | IMMUNOGC_C4839 | GAPDH | mRNA | 0 |  | Metabolism of carbohydrates | hsa01100;hsa04066;hsa05010 |  | GAPDH | NA | azure4 | 1 | 0.436974789915966
  G6PD-mRNA | -0.00084 | 0.0313 | -0.0621 | 0.0605 | 0.999 | 0.958 | 1.04 | 0.979 | 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 | -0.0268370607028754

  ##### DE Results - Metabolism of carbohydrates genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  DROSHA-mRNA | 0.0504 | 0.0237 | 0.00396 | 0.0969 | 1.04 | 1 | 1.07 | 0.0361 | 0.918 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DROSHA | mRNA | 0 |  | MicroRNA (miRNA) biogenesis | hsa05205 |  | DROSHA | NA | azure4 | 1 | 2.12658227848101
  TARBP2-mRNA | 0.0423 | 0.0255 | -0.00766 | 0.0922 | 1.03 | 0.995 | 1.07 | 0.1 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | TARBP2 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | TARBP2 | NA | azure4 | 1 | 1.65882352941176
  XPO5-mRNA | 0.0389 | 0.024 | -0.0081 | 0.0859 | 1.03 | 0.994 | 1.06 | 0.108 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | XPO5 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | XPO5 | NA | azure4 | 1 | 1.62083333333333
  DGCR8-mRNA | 0.0167 | 0.0322 | -0.0464 | 0.0797 | 1.01 | 0.968 | 1.06 | 0.606 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DGCR8 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis |  |  | DGCR8 | NA | azure4 | 1 | 0.518633540372671
  DICER1-mRNA | 0.00568 | 0.0286 | -0.0504 | 0.0618 | 1 | 0.966 | 1.04 | 0.843 | 1 | lm.nb | MicroRNA (miRNA) biogenesis | IMMUNOGC_C4839 | DICER1 | mRNA | 0 |  | MicroRNA (miRNA) biogenesis | hsa05206 |  | DICER1 | NA | azure4 | 1 | 0.198601398601399

  ##### DE Results - MicroRNA (miRNA) biogenesis genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  MAPK11-mRNA | 0.0545 | 0.0267 | 0.00226 | 0.107 | 1.04 | 1 | 1.08 | 0.0437 | 0.961 | 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 | 2.04119850187266
  JUN-mRNA | 0.058 | 0.0284 | 0.00236 | 0.114 | 1.04 | 1 | 1.08 | 0.0438 | 0.961 | 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 | 2.04225352112676
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  NFKB1-mRNA | 0.0359 | 0.0212 | -0.0056 | 0.0774 | 1.03 | 0.996 | 1.06 | 0.0933 | 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 | 1.69339622641509
  RELA-mRNA | 0.0288 | 0.023 | -0.0162 | 0.0739 | 1.02 | 0.989 | 1.05 | 0.213 | 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 | 1.25217391304348
  MAPK8-mRNA | 0.0276 | 0.0234 | -0.0182 | 0.0734 | 1.02 | 0.987 | 1.05 | 0.24 | 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 | 1.17948717948718
  MAPK14-mRNA | 0.0225 | 0.0256 | -0.0278 | 0.0728 | 1.02 | 0.981 | 1.05 | 0.383 | 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 | 0.87890625
  NFKBIA-mRNA | -0.0216 | 0.0314 | -0.0831 | 0.0399 | 0.985 | 0.944 | 1.03 | 0.493 | 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 | -0.687898089171975

  ##### DE Results - MyD88.CL.Mal cascade initiated on plasma membrane genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  CXCL5-mRNA | 0.103 | 0.0387 | 0.0276 | 0.179 | 1.07 | 1.02 | 1.13 | 0.00884 | 0.411 | 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 | slateblue4 | 16 | 2.66149870801034
  Cxcl10-mRNA | -0.0625 | 0.0276 | -0.117 | -0.00836 | 0.958 | 0.922 | 0.994 | 0.026 | 0.826 | 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 | -2.26449275362319
  CCR5-mRNA | 0.0551 | 0.0244 | 0.00725 | 0.103 | 1.04 | 1.01 | 1.07 | 0.0264 | 0.826 | 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 | 2.25819672131148
  Ccl2-mRNA | 0.0683 | 0.0306 | 0.00826 | 0.128 | 1.05 | 1.01 | 1.09 | 0.0282 | 0.826 | 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 | 2.23202614379085
  CXCR4-mRNA | 0.0595 | 0.0288 | 0.00298 | 0.116 | 1.04 | 1 | 1.08 | 0.0419 | 0.961 | 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 | 2.06597222222222
  Ccl4-mRNA | -0.0613 | 0.032 | -0.124 | 0.00133 | 0.958 | 0.918 | 1 | 0.0581 | 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 | -1.915625
  PMCH-mRNA | 0.0422 | 0.023 | -0.00282 | 0.0873 | 1.03 | 0.998 | 1.06 | 0.0694 | 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 | 1.83478260869565
  NMUR1-mRNA | 0.0412 | 0.0252 | -0.00819 | 0.0905 | 1.03 | 0.994 | 1.06 | 0.105 | 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 | 1.63492063492063
  CXCR6-mRNA | 0.0362 | 0.0249 | -0.0126 | 0.0851 | 1.03 | 0.991 | 1.06 | 0.149 | 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 | 1.45381526104418
  ANXA1-mRNA | 0.0293 | 0.0203 | -0.0104 | 0.069 | 1.02 | 0.993 | 1.05 | 0.151 | 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 | 1.44334975369458
  FPR2-mRNA | -0.0284 | 0.0277 | -0.0826 | 0.0259 | 0.981 | 0.944 | 1.02 | 0.308 | 1 | 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 | azure4 | 1 | -1.02527075812274
  CCR3-mRNA | 0.0256 | 0.0284 | -0.0301 | 0.0812 | 1.02 | 0.979 | 1.06 | 0.37 | 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 | 0.901408450704225
  Ccl3-mRNA | 0.0186 | 0.0352 | -0.0504 | 0.0875 | 1.01 | 0.966 | 1.06 | 0.599 | 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 | 0.528409090909091
  CXCL8-mRNA | 0.017 | 0.0522 | -0.0854 | 0.119 | 1.01 | 0.943 | 1.09 | 0.746 | 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 | 0.325670498084291
  CCR2-mRNA | 0.00219 | 0.0205 | -0.0379 | 0.0423 | 1 | 0.974 | 1.03 | 0.915 | 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 | 0.106829268292683

  ##### DE Results - Peptide ligand-binding receptors genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | 0.148 | 0.022 | 0.105 | 0.192 | 1.11 | 1.08 | 1.14 | 1.32e-09 | 5.95e-07 | 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 | slateblue1 | 16 | 6.72727272727273
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - RAF-independent MAPK13 activation genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - RAFMAP kinase cascade genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MS4A2-mRNA | 0.0778 | 0.0364 | 0.00641 | 0.149 | 1.06 | 1 | 1.11 | 0.0353 | 0.918 | 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 | 2.13736263736264
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792

  ##### DE Results - Role of LAT2NTALLAB on calcium mobilization genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | 0.148 | 0.022 | 0.105 | 0.192 | 1.11 | 1.08 | 1.14 | 1.32e-09 | 5.95e-07 | 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 | slateblue1 | 16 | 6.72727272727273
  JUN-mRNA | 0.058 | 0.0284 | 0.00236 | 0.114 | 1.04 | 1 | 1.08 | 0.0438 | 0.961 | 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 | 2.04225352112676
  CXCL8-mRNA | 0.017 | 0.0522 | -0.0854 | 0.119 | 1.01 | 0.943 | 1.09 | 0.746 | 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 | 0.325670498084291
  CEBPB-mRNA | -0.0032 | 0.0222 | -0.0467 | 0.0403 | 0.998 | 0.968 | 1.03 | 0.886 | 1 | 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 | azure4 | 1 | -0.144144144144144

  ##### DE Results - Senescence-Associated Secretory Phenotype (SASP) genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  THBS1-mRNA | 0.0582 | 0.0369 | -0.014 | 0.13 | 1.04 | 0.99 | 1.09 | 0.118 | 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 | 1.57723577235772
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  STAT6-mRNA | -0.0147 | 0.0335 | -0.0804 | 0.0509 | 0.99 | 0.946 | 1.04 | 0.661 | 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 | -0.438805970149254
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - Signaling by PDGF genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  CD28-mRNA | 0.0586 | 0.0218 | 0.0159 | 0.101 | 1.04 | 1.01 | 1.07 | 0.00842 | 0.411 | 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 | slateblue4 | 16 | 2.68807339449541
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  AGO2-mRNA | 0.0383 | 0.0265 | -0.0136 | 0.0903 | 1.03 | 0.991 | 1.06 | 0.151 | 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 | 1.44528301886792
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - Signaling by SCF-KIT genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  Rit1-mRNA | 0.0959 | 0.0265 | 0.044 | 0.148 | 1.07 | 1.03 | 1.11 | 0.000473 | 0.0491 | lm.nb | Signalling to p38 via RIT and RIN | IMMUNOGC_C4839 | Rit1 | mRNA | 0 |  | Signalling to p38 via RIT and RIN |  |  | RIT1 | NA | slateblue3 | 16 | 3.6188679245283
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - Signalling to p38 via RIT and RIN genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | 0.116 | 0.0282 | 0.061 | 0.171 | 1.08 | 1.04 | 1.13 | 8.14e-05 | 0.011 | 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 | slateblue2 | 16 | 4.11347517730496
  TNFRSF17-mRNA | -0.0752 | 0.0253 | -0.125 | -0.0256 | 0.949 | 0.917 | 0.982 | 0.00377 | 0.231 | 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 | slateblue4 | 16 | -2.97233201581028
  CD40LG-mRNA | 0.053 | 0.0237 | 0.00657 | 0.0995 | 1.04 | 1 | 1.07 | 0.0276 | 0.826 | 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 | 2.23628691983122
  LTA-mRNA | 0.0524 | 0.0251 | 0.00324 | 0.102 | 1.04 | 1 | 1.07 | 0.0394 | 0.949 | 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 | 2.08764940239044
  Tnfsf4-mRNA | 0.0723 | 0.0357 | 0.00235 | 0.142 | 1.05 | 1 | 1.1 | 0.0457 | 0.961 | 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 | 2.02521008403361
  TNFRSF18-mRNA | 0.0434 | 0.0327 | -0.0206 | 0.107 | 1.03 | 0.986 | 1.08 | 0.187 | 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 | 1.32721712538226
  CD27-mRNA | 0.0273 | 0.0211 | -0.014 | 0.0685 | 1.02 | 0.99 | 1.05 | 0.199 | 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 | 1.29383886255924
  CD40-mRNA | 0.0346 | 0.0319 | -0.028 | 0.0971 | 1.02 | 0.981 | 1.07 | 0.281 | 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 | 1.0846394984326
  RELB-mRNA | 0.0169 | 0.0248 | -0.0317 | 0.0655 | 1.01 | 0.978 | 1.05 | 0.497 | 1 | 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 | 0.681451612903226

  ##### DE Results - TNFR2 non-canonical NF-kB pathway genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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 | 0.116 | 0.0282 | 0.061 | 0.171 | 1.08 | 1.04 | 1.13 | 8.14e-05 | 0.011 | 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 | slateblue2 | 16 | 4.11347517730496
  TNFRSF17-mRNA | -0.0752 | 0.0253 | -0.125 | -0.0256 | 0.949 | 0.917 | 0.982 | 0.00377 | 0.231 | 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 | slateblue4 | 16 | -2.97233201581028
  LTA-mRNA | 0.0524 | 0.0251 | 0.00324 | 0.102 | 1.04 | 1 | 1.07 | 0.0394 | 0.949 | 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 | 2.08764940239044
  Tnfsf4-mRNA | 0.0723 | 0.0357 | 0.00235 | 0.142 | 1.05 | 1 | 1.1 | 0.0457 | 0.961 | 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 | 2.02521008403361
  TNFRSF18-mRNA | 0.0434 | 0.0327 | -0.0206 | 0.107 | 1.03 | 0.986 | 1.08 | 0.187 | 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 | 1.32721712538226
  CD27-mRNA | 0.0273 | 0.0211 | -0.014 | 0.0685 | 1.02 | 0.99 | 1.05 | 0.199 | 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 | 1.29383886255924

  ##### DE Results - TNFs bind their physiological receptors genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  Klf4-mRNA | -0.0447 | 0.022 | -0.0879 | -0.00156 | 0.969 | 0.941 | 0.999 | 0.0451 | 0.961 | lm.nb | Transcriptional regulation of white adipocyte differentiation | IMMUNOGC_C4839 | Klf4 | mRNA | 0 |  | Transcriptional regulation of white adipocyte differentiation | hsa04550 |  | KLF4 | NA | azure4 | 1 | -2.03181818181818
  TGFB1-mRNA | 0.0267 | 0.0337 | -0.0393 | 0.0928 | 1.02 | 0.973 | 1.07 | 0.43 | 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 | 0.792284866468843
  Egr2-mRNA | -0.00738 | 0.0279 | -0.0621 | 0.0473 | 0.995 | 0.958 | 1.03 | 0.792 | 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 | -0.264516129032258
  CEBPB-mRNA | -0.0032 | 0.0222 | -0.0467 | 0.0403 | 0.998 | 0.968 | 1.03 | 0.886 | 1 | 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 | azure4 | 1 | -0.144144144144144

  ##### DE Results - Transcriptional regulation of white adipocyte differentiation genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  AKT3-mRNA | 0.0792 | 0.0232 | 0.0338 | 0.125 | 1.06 | 1.02 | 1.09 | 0.000936 | 0.0894 | 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 | slateblue3 | 16 | 3.41379310344828
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  VEGFA-mRNA | -0.0528 | 0.0243 | -0.1 | -0.00511 | 0.964 | 0.933 | 0.996 | 0.0326 | 0.878 | 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 | -2.17283950617284
  MAPK11-mRNA | 0.0545 | 0.0267 | 0.00226 | 0.107 | 1.04 | 1 | 1.08 | 0.0437 | 0.961 | 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 | 2.04119850187266
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  MAPK13-mRNA | 0.0316 | 0.0276 | -0.0224 | 0.0856 | 1.02 | 0.985 | 1.06 | 0.254 | 1 | 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 | 1.14492753623188
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - VEGFA-VEGFR2 Pathway genes - BMI

  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.

BMI:
- BMI

- Volcano Plot: BMI
  More Plot Information

  ##### Volcano Plot: BMI

  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 - BMI
  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
  IL2RA-mRNA | 0.0985 | 0.0266 | 0.0464 | 0.151 | 1.07 | 1.03 | 1.11 | 0.00036 | 0.0404 | 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 | slateblue2 | 16 | 3.70300751879699
  KIT-mRNA | 0.0805 | 0.0248 | 0.0318 | 0.129 | 1.06 | 1.02 | 1.09 | 0.00165 | 0.131 | 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 | slateblue4 | 16 | 3.24596774193548
  MAPK1-mRNA | 0.0554 | 0.0224 | 0.0115 | 0.0993 | 1.04 | 1.01 | 1.07 | 0.0153 | 0.589 | 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 | 2.47321428571429
  NEFL-mRNA | 0.0646 | 0.0269 | 0.0119 | 0.117 | 1.05 | 1.01 | 1.08 | 0.0183 | 0.666 | 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 | 2.40148698884758
  VEGFA-mRNA | -0.0528 | 0.0243 | -0.1 | -0.00511 | 0.964 | 0.933 | 0.996 | 0.0326 | 0.878 | 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 | -2.17283950617284
  MAP2K1-mRNA | 0.0411 | 0.0203 | 0.00121 | 0.0809 | 1.03 | 1 | 1.06 | 0.0463 | 0.961 | 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 | 2.02463054187192
  Dusp5-mRNA | 0.0328 | 0.0287 | -0.0234 | 0.089 | 1.02 | 0.984 | 1.06 | 0.255 | 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 | 1.14285714285714
  IL5RA-mRNA | 0.0265 | 0.0262 | -0.0249 | 0.0779 | 1.02 | 0.983 | 1.06 | 0.315 | 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 | 1.01145038167939
  NCAM1-mRNA | 0.0188 | 0.027 | -0.0341 | 0.0716 | 1.01 | 0.977 | 1.05 | 0.488 | 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 | 0.696296296296296
  IL3-mRNA | 0.00922 | 0.0242 | -0.0382 | 0.0567 | 1.01 | 0.974 | 1.04 | 0.704 | 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 | 0.38099173553719
  IL3RA-mRNA | -0.00481 | 0.024 | -0.0518 | 0.0422 | 0.997 | 0.965 | 1.03 | 0.841 | 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 | 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 | -0.200416666666667
  DUSP1-mRNA | 0.006 | 0.0323 | -0.0574 | 0.0694 | 1 | 0.961 | 1.05 | 0.853 | 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 | 0.185758513931889

  ##### DE Results - VEGFR2 mediated cell proliferation genes - BMI

  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

BMI:
- BMI

Pathways:

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

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

- 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 BMI.

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 BMI.

- 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 BMI.

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. BMI
  More Plot Information

  ##### Raw cell type measurements vs. BMI

  Plots the raw cell type abundance measurements against BMI.

- T-cells Measurement vs. BMI
  More Plot Information

  ##### T-cells Measurement vs. BMI

  Plots T-cells measurements against BMI.

- DC Measurement vs. BMI
  More Plot Information

  ##### DC Measurement vs. BMI

  Plots DC measurements against BMI.

- NK cells Measurement vs. BMI
  More Plot Information

  ##### NK cells Measurement vs. BMI

  Plots NK cells measurements against BMI.

- B-cells Measurement vs. BMI
  More Plot Information

  ##### B-cells Measurement vs. BMI

  Plots B-cells measurements against BMI.

- NK CD56dim cells Measurement vs. BMI
  More Plot Information

  ##### NK CD56dim cells Measurement vs. BMI

  Plots NK CD56dim cells measurements against BMI.

- Cytotoxic cells Measurement vs. BMI
  More Plot Information

  ##### Cytotoxic cells Measurement vs. BMI

  Plots Cytotoxic cells measurements against BMI.

- CD8 T cells Measurement vs. BMI
  More Plot Information

  ##### CD8 T cells Measurement vs. BMI

  Plots CD8 T cells measurements against BMI.

- Macrophages Measurement vs. BMI
  More Plot Information

  ##### Macrophages Measurement vs. BMI

  Plots Macrophages measurements against BMI.

- Mast cells Measurement vs. BMI
  More Plot Information

  ##### Mast cells Measurement vs. BMI

  Plots Mast cells measurements against BMI.

- Th1 cells Measurement vs. BMI
  More Plot Information

  ##### Th1 cells Measurement vs. BMI

  Plots Th1 cells measurements against BMI.

- Neutrophils Measurement vs. BMI
  More Plot Information

  ##### Neutrophils Measurement vs. BMI

  Plots Neutrophils measurements against BMI.

- Treg Measurement vs. BMI
  More Plot Information

  ##### Treg Measurement vs. BMI

  Plots Treg measurements against BMI.

Choose a Cell Type:

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

- Relative cell type measurements vs. BMI
  More Plot Information

  ##### Relative cell type measurements vs. BMI

  Plots the relative cell type abundance measurements against BMI.

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

  ##### CD8.vs..Treg Measurement vs. BMI

  Plots CD8.vs..Treg measurements against BMI.

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

  ##### CD4.vs..T.cells Measurement vs. BMI

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

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

##### Analysis Details

Analysis name: New Analysis 21
Location of results: C:\Users\Jeff\Desktop\nSolver
File type of plots: png

##### Sample Annotation Details

Unique sample identifier: File.Name
Covariate1: BMI; Variable Type: continuous; Reference Level: NA

##### 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: BMI

##### Differential Expression Analysis Details

Perform differential expression testing: TRUE
Predictors: BMI
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: BMI
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.