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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.