Eiteneuer, C.; Velasco, D.; Atemia, J.; Wang, D.; Schwacke, R.; Wahl, V.; Schrader, A.; Reimer, J.J.; Fahrner, S.; Pieruschka, R.; Schurr, U.; Usadel, B.; Hallab, A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. Plants2022, 11, 745.
Eiteneuer, C.; Velasco, D.; Atemia, J.; Wang, D.; Schwacke, R.; Wahl, V.; Schrader, A.; Reimer, J.J.; Fahrner, S.; Pieruschka, R.; Schurr, U.; Usadel, B.; Hallab, A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. Plants 2022, 11, 745.
Eiteneuer, C.; Velasco, D.; Atemia, J.; Wang, D.; Schwacke, R.; Wahl, V.; Schrader, A.; Reimer, J.J.; Fahrner, S.; Pieruschka, R.; Schurr, U.; Usadel, B.; Hallab, A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. Plants2022, 11, 745.
Eiteneuer, C.; Velasco, D.; Atemia, J.; Wang, D.; Schwacke, R.; Wahl, V.; Schrader, A.; Reimer, J.J.; Fahrner, S.; Pieruschka, R.; Schurr, U.; Usadel, B.; Hallab, A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. Plants 2022, 11, 745.
Abstract
Next generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever growing number of life science research projects. Typically, well established software pipelines provide quantitative data informing about gene expression or concentrations of metabolites from the raw data. This data needs to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some tools exist, but require installation or manual programming. We developed “Gene Expression Plotter” (GXP), an RNA-Seq and Metabolomics data visualization and analysis tool entirely running in the user’s web browsers, thus not needing any custom installation, manual programming or upload of confidential data to third party servers. GXP enables the user to generate interactive plots, visually summarize genetic or metabolic responses in scientific sketches (Mapman), carry out cluster and principal component analysis, and conduct overrepresentation analyses. GXP can be used to publish research data along with interactive plots and results of analyses carried out with it. GXP is freely available on GitHub: https://github.com/usadellab/GeneExpressionPlots
Keywords
RNA sequencing; metabolomics; data visualization; overrepresentation analysis; cluster analysis; principal component analysis; scientific plotting; Mapman; Mercator
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.