Table 3 Overview of tested pathway enrichment methods
From: SEMgsa: topology-based pathway enrichment analysis with structural equation models
Method | Null hypothesis | Gene p value tresholding | Expression data | Pathway | R/Bioconductor [References] |
|---|---|---|---|---|---|
SEMgsa | Self-contained | No | Yes | Topology | SEMgraph 1.1.1 [17] |
DEGraph | Self-contained | No | Yes | Topology | DEGraph 1.46.0 [14] |
TopologyGSA | Self-contained | No | Yes | Topology | TopologyGSA 1.4.7 [13] |
NetGSA | Self-contained | No | Yes | Topology | |
PathwayExpress | Competitive | Optional | No | Topology | |
ORA | Competitive | Yes | No | Membership | EnrichmentBrowser 2.25.3 [1] |