A comparative study of topology-based pathway enrichment analysis methods

BMC Bioinformatics

Table 1 Overview of tested pathway enrichment methods

Method	Null hypothesis	Gene p-value thresholding	Expression data	Pathway	R/Bioconductor	Reference
Pathway-Express	Competitive	Optional	No	Topology	ROntoTools 2.10.0	[8]
SPIA	Competitive	Yes	No	Topology	graphite 1.28.2	[9]
NetGSA	Self-contained	No	Yes	Topology	netgsa 3.1.0	[10, 11]
topologyGSA	Self-contained	No	Yes	Topology	topologyGSA 1.4.6	[12]
DEGraph	Self-contained	No	Yes	Topology	DEGraph 1.34.0	[13]
CAMERA	Competitive	No	Yes	Membership	limma 3.38.3	[14]
CePa	Competitive	Yes	No	Topology	CePa 0.6	[15, 48]
PRS	Competitive	Yes	No	Topology	ToPASeq 1.16.1	[16, 51]
PathNet	Competitive	Yes	No	Topology	PathNet 1.22.0	[17]

All methods return the p-values before and/or after correcting for multiple comparisons

ISSN: 1471-2105