Introduction

Gene Set Context Analysis (GSCA) is an open source software package to help researchers use massive amounts of publicly available gene expression data (PED) to make discoveries. Users can interactively visualize and explore gene and gene set activities in 25,000+ consistently normalized human and mouse gene expression samples representing diverse biological contexts (e.g. different cells, tissues and disease types, etc.). By providing one or multiple genes or gene sets as input and specifying a gene set activity pattern of interest, users can query the expression compendium to systematically identify biological contexts associated with the specified gene set activity pattern. In this way, researchers with new gene sets from their own experiments may discover previously unknown contexts of gene set functions and hence increase the value of their experiments. GSCA has a graphical user interface (GUI). The GUI makes the analysis convenient and customizable. Analysis results can be conveniently exported as publication quality figures and tables. GSCA is available at https://github.com/zji90/GSCA. This software significantly lowers the bar for biomedical investigators to use PED in their daily research for generating and screening hypotheses, which was previously difficult because of the complexity, heterogeneity and size of the data.

Publications

  1. Turning publicly available gene expression data into discoveries using gene set context analysis.
    Cite this
    Ji Z, Vokes SA, Dang CV, Ji H, 2016-01-01 - Nucleic acids research

Credits

  1. Zhicheng Ji
    Developer

    Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, United States of America

  2. Steven A Vokes
    Developer

    Department of Molecular Biosciences, The University of Texas at Austin, United States of America

  3. Chi V Dang
    Developer

    Abramson Cancer Center, University of Pennsylvania, United States of America

  4. Hongkai Ji
    Investigator

    Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, United States of America

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Summary
AccessionBT001891
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByHongkai Ji