GXP: Analyze and Plot Plant Omics Data in Web Browsers

Plants, vol. 11, pp. 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, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed "Gene Expression Plotter" (GXP), an RNAseq and Metabolomics data visualization and analysis tool entirely running in the user's web browser, thus not needing any custom installation, manual programming or uploading of confidential data to third party servers. Consequently, upon receiving the bioinformatic raw data analysis of RNAseq or other omics results, GXP immediately enables the user to interact with the data according to biological questions by performing knowledge-driven, in-depth data analyses and candidate identification via visualization and data exploration. Thereby, GXP can support and accelerate complex interdisciplinary omics projects and downstream analyses. GXP offers an easy way to publish data, plots, and analysis results either as a simple exported file or as a custom website. GXP is freely available on GitHub (see introduction).

Authors 13

1. Constantin Eiteneuer

   Forschungszentrum Jülich

   Affiliation as printed

   IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany

2. David Velasco

   Norwegian University of Science and Technology

   Affiliation as printed

   Faculty of Natural Sciences, Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, Norway

3. Joseph Atemia

   Forschungszentrum Jülich

   Affiliation as printed

   IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany

4. Dan Wang

   Forschungszentrum Jülich

   Affiliation as printed

   IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany

5. Rainer Schwacke

   Forschungszentrum Jülich

   Affiliation as printed

   IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany

6. Vanessa Wahl

   Max Planck Institute of Molecular Plant Physiology

   Affiliation as printed

   Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany

7. Andrea Schrader Aachen Institute for Biology I

   RWTH Aachen University

   Affiliation as printed

   Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany

8. Julia J. Reimer Aachen Institute for Biology I

   University of Applied Sciences Emden Leer · RWTH Aachen University

   Affiliation as printed

   Faculty of Technology, University of Applied Science Emden/Leer, Molecular Biosciences, 26723 Emden, Germany

   Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany

9. Sven Fahrner

   Forschungszentrum Jülich

   Affiliation as printed

   IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany

10. Roland Pieruschka

    Forschungszentrum Jülich

    Affiliation as printed

    IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany

11. Ulrich Schurr

    Forschungszentrum Jülich

    Affiliation as printed

    IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany

12. Björn Usadel

    Forschungszentrum Jülich

    Affiliation as printed

    IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany

13. Asis Hallab corresponding

    Forschungszentrum Jülich

    Affiliation as printed

    IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany