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Table 1 Overview of different competitive gene set methods

From: Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

Principle Method Reference Test type Software
Over-representation analysis (hypergeometric test) [67] parametric GOstats
GSEA [68] non-parametric GSEABase
  [27] non-parametric http://www.broad.mit.edu/gsea
GSA [69] non-parametric http://cran.r-project.org/web/packages/GSA/
GSEArot [70] non-parametric limma
GAGE [71] parametric GAGE
PAGE [72] parametric PGSEA, GAGE
Random Set [73] parametric part of CLEAN
Generalized Random Sets [74] parametric http://GenomicsPortals.org
Gene set enrichment analysis made simple [75] parametric  
  1. If available, the name of the software package is provided.