GSEA v2.1.0. Release Notes

GSEA v2.1.0 has the following upgrades:

1. In collaboration with the Bader lab at the University of Toronto, we have added Enrichment Map visualization as one of the steps in a GSEA analysis. Enrichment Map visualization organizes gene sets into a network work two gene sets are connected in the enrichment map if they have high overlap, i.e., if they share many of the same genes. Applying automatic layout techniques, groups of inter-related gene sets will tend to cluster together, providing a much easier and intuitive visualization of the enrichment results. For example, the resulting enrichment map might reveal distinct clusters of gene sets associated with the Cell Cycle, Transcription, Translation, DNA Metabolism, etc.
2. Improved text describing error 1001. Now reads "After pruning, none of the gene sets passed size thresholds". This communicates that tests to determine whether gene sets pass size threshold are done AFTER gene sets have been pruned to remove genes that do not appear in the gebe expression data file or ranked gene list file.
3. There is now a button on GSEA's main user interface for initiating the creation of an enrichment map of GSEA results directly from the GSEA desktop application. Users can create multiple enrichment maps from this interface; they can also compare two different enrichment results within a single map.
4. Further information on this feature, along with guided, step-by-step tutorial, is available here