GSEALeadingEdgeViewer (v5)

Description

Displays four graphs to help visualize leading-edge subsets of selected gene sets in GSEA results.

Module Summary

For a full description of the GSEA algorithm, refer to the GSEA GenePattern module documentation or the GSEA User Guide.

As described in the Gene Set Enrichment Analysis (GSEA) paper (see References), the "leading edge" describes a subset of genes in a gene set. This subset contains the genes that appear in the ranked gene set list between zero and the point at which the running sum statistic reaches its greatest deviation from zero, as shown in the following figure.

The leading-edge subset can be interpreted as the core group of genes that accounts for the gene set’s enrichment signal.

This visualizer displays four graphs that help you visualize the overlap between the leading-edge subsets of selected gene sets.  You can also use the visualizer to generate an HTML report of the Leading Edge Analysis.

For more information on the leading edge analysis, see Interpreting leading edge analysis results in the GSEA User Guide.

References

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS. 2005;102(43);15545-15550. (link)

Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesivor JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC.  PGC-1-α responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34:267-273. (link)

GSEA User Guide: http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html

Parameters

Input Files

1. input file name: ZIP

ZIP file produced by GSEA module containing the result files.  

Task Type:
Visualizer

CPU Type:
any

Operating System:
any

Language:
Java