New & Improved in GSEA Desktop Application Version 2

Version 2 of the GSEA Java desktop software (GSEA-P) contains a complete implementation of the GSEA methodology including leading edge analysis, an integrated MSigDB set browser, improved annotation and mapping tools as well as several usability improvements based on user feedback (Subramanian et al., 2007).

The GSEA algorithm has not changed. The implementation remains as described in Subramanian, Tamayo, et al. (2005).

New and improved features include:

Run GSEA panel

  • Collapse dataset option converts native probe ids to gene symbols as part of the enrichment analysis

Enrichment reports

  • Enrichment plot includes a color bar that depicts phenotype correlation based on ranking metric scores

  • Snapshot page shows enrichment plots for the top 20 enriched gene sets (or for the number you specify)

  • For MSigDB gene sets, hyperlinks to the Gene Set Cards are automatically inserted in the report

  • Gene marker permutation report allows easy comparison of genes and gene sets

Leading edge analysis

  • Enrichment reports show the leading edge subsets for enriched gene sets; that is, the genes in the gene set that are driving the enrichment results

  • Leading edge analysis compares leading edge subsets across gene sets, revealing which gene sets correspond to the same biological process and which represent distinct processes.

New MSigDB release

  • >3000 gene sets

  • Pathways curated from 15 different sources

  • >1600 signatures curated from published transcriptional profiles

MSigDB gene sets browser

  • Browse MSigDB gene sets from within the GSEA application

  • Search for gene sets in several ways including by category or by keyword

  • Download selected gene sets to GSEA-formatted gene set files

Annotations in the form of Gene set Cards

  • Gene set cards provide extensive annotation about the derivation of a gene set including source, category and PubMedID

  • Sequence motif based gene sets matched to TRANSFAC annotations

    Chip2Chip: map gene sets between platforms

  • Convert gene sets between gene symbols and chip platforms, or between chip platforms

  • 93 chip platforms supported
  • collapse

    Chip annotations

    • New microarray platforms added for a total of 93 supported platforms

    • Chip annotation (*.chip) files available on the Broad ftp site

    • Custom chip annotations can be added by creating your own .chip files

    Application usability

    • Object browser displays datasets currently in memory

    • The application base directory (gsea_home) can be installed anywhere on the file system and its location specified by a preference setting

    Batch analysis mode

    • Command line usage simplified by adding defaults for algorithm parameters
    • Heat maps and all other visualizations work from the command line


    • Comprehensive user guide
    • Software tutorial
    • FAQ
    Download GSEA 2.0