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GGEA - Gene Graph Enrichment Analysis

GGEA is an intuitive method to detect consistently and coherently enriched gene sets, based on prior knowledge derived from directed gene regulatory networks. GGEA comes embedded in the EnrichmentBrowser system, a powerful multi-functional framework for enrichment analysis of gene expression data. Currently the following enrichment analysis methods are supported:
  • ORA Overrepresentation Analysis (based on the hypergeometric distribution)
  • SAFE Significance Analysis of Function and Expression (Barry et al., 2005, Bioinformatics, 21:1943-9)
  • GSEA Gene Set Enrichment Analysis (Subramanian et al., 2005, Proc. Natl. Acad. Sci. USA, 102:15545-15550)
  • SAMGS Significance Analysis of Microarrays on Gene Sets (Dinu et al., 2007, BMC Bioinformatics, 8:242)
  • SPIA Signaling Pathway Impact Analysis (Tarca et al., 2009, Bioinformatics, 25(1):75-82)
  • GGEA Gene Graph Enrichment Analysis (Geistlinger et al., 2011, Bioinformatics, 27(13):i366-i373)

GGEA and the EnrichmentBrowser are freely available under the GNU Lesser General Public License (LGPL).

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