GSCA

Gene Set Context Analysis (GSCA) is an open-source software to leverage the vast amounts of publicly available gene expression data (PED) for research discovery. It offers an interactive platform for visualizing and exploring the activities of genes and gene sets across over 25,000 normalized human and mouse gene expression samples from various biological contexts, such as different cell types, tissues, and diseases.

Users can input one or multiple genes or gene sets and specify an activity pattern to systematically identify biological contexts where the gene set exhibits the specified pattern. This feature enables researchers to uncover new contexts for gene set functions, enhancing the value of their experimental findings. GSCA's graphical user interface (GUI) simplifies analysis, allowing for customization and easy export of results in publication-quality formats.

Topic

Gene expression;Molecular genetics

Detail

  • Operation: Enrichment analysis;Gene expression analysis

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 2.32.0

  • Credit: The National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: Zhicheng Ji zji4@jhu.edu

  • Collection: -

  • Maturity: Stable

Publications

  • Turning publicly available gene expression data into discoveries using gene set context analysis.
  • Ji Z, et al. Turning publicly available gene expression data into discoveries using gene set context analysis. Turning publicly available gene expression data into discoveries using gene set context analysis. 2016; 44:e8. doi: 10.1093/nar/gkv873
  • https://doi.org/10.1093/nar/gkv873
  • PMID: 26350211
  • PMC: PMC4705686

Download and documentation

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