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Table 2 Overview of self-contained gene set and pathway methods

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

Principle Method Reference Software
Average of single-gene statistics [79] sigPathway
Linear Model Toolset for GSEA [80] GSEAlm
SAM-GS [81]  
Globaltest [82] globaltest
GlobalANCOVA [83] GlobalAncova
Hotelling’s T2 [8487] PCOT2
N-statistic [88] cramer
RCMAT [89]  
Non-linear tests for identifying differentially expressed genes or genetic networks [87]  
Pathway-express [90]  
Signaling Pathway Impact Analysis [91] SPIA (Bioconductor)
SEPEA [92]  
PARADIGM [93]  
Gene set analysis exploiting the topology of a pathway [94] IPS (available upon request)