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

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

[84–87]

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)