GXP: Analyze and Plot Plant Omics Data in Web Browsers
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
Authors 11
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Affiliation as printed
Affiliation 1 ; IBG-
; IBG-
Affiliation
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Norwegian University of Science and Technology
Affiliation as printed
; Norges Teknisk-Naturvitenskapelige Universitet , 7034 Trondheim , Norway
Affiliation
; Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, Norway
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Affiliation as printed
Affiliation 2 ; IBG-4 Bioinformatics , Forschungszentrum Jülich , 52428 Jülich , Germany
Plant Sciences , Forschungszentrum Jülich , 52428 Jülich , Germany
; IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
Affiliation
Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany
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Affiliation as printed
; RWTH Aachen University , Institute for Biology I , 52062 Aachen , Germany
Affiliation
; RWTH Aachen University, Institute for Biology I, 52062 Aachen, Germany
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Affiliation as printed
Affiliation 1 ; IBG-
; IBG-
Affiliation
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Affiliation as printed
Affiliation 1 ; IBG-
; IBG-
Affiliation
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Affiliation as printed
Affiliation 2 ; IBG-4 Bioinformatics , Forschungszentrum Jülich , 52428 Jülich , Germany
Plant Sciences , Forschungszentrum Jülich , 52428 Jülich , Germany
; IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
Affiliation
Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany
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Max Planck Institute of Molecular Plant Physiology
Affiliation as printed
; Max Planck Institute for Molecular Plant Physiology , 14476 Potsdam , Germany
Affiliation
; Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
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Affiliation as printed
Affiliation 1 ; IBG-
; IBG-
Affiliation
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Affiliation as printed
Affiliation 2 ; IBG-4 Bioinformatics , Forschungszentrum Jülich , 52428 Jülich , Germany
Plant Sciences , Forschungszentrum Jülich , 52428 Jülich , Germany
; IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
Affiliation
Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany
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Asis Hallab corresponding
Affiliation as printed
Affiliation 2 ; IBG-4 Bioinformatics , Forschungszentrum Jülich , 52428 Jülich , Germany
Plant Sciences , Forschungszentrum Jülich , 52428 Jülich , Germany
; IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
Affiliation
Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany
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