Table 1.

Pathway enrichment methods for interpreting pathways characteristic of an experimental gene list

Tools	Statistical approach	Pathway database	PMID
GO-Elite	Hypergeometric distribution and Fisher’s exact test	Gene Ontology, WikiPathways, KEGG, microRNA, user defined	22743224
GeneTrail	Hypergeometric distribution and Fisher’s exact test	KEGG, TRANSPATH, Gene Ontology, DIP	17526521
ConceptGen	Modified Fisher’s exact test	Gene Ontology, MiMI, KEGG, Panther, BioCarta	21715386
KOBAS 2.0	Binomial test, chi-square test, Fisher’s exact test and hypergeometric test	KEGG, PID curated, PID BioCarta, PID Reactome, BioCyc, Panther	21715386
DAVID	Kappa statistics	Gene Ontology, PANTHER, BIND, MINT, DIP	17576678
Enrichr	Fisher’s exact test and z score of the deviation from the expected rank by the Fisher’s exact test	NCI-Nature, PANTHER, metabolic pathway, Gene Ontology, BioCarta, user defined	23586463 27141961
NEA	Use z score to compute the enrichment statistics based on the interactome network topology	KEGG, Gene Ontology, user defined	28361684
TopoGSA	Target genes are mapped to an interaction network to compute topological properties and are compared with pathway genes	PPI network, KEGG, BioCarta, Gene Ontology	20335277
TPEA	TPEA measures topological properties of pathways of the genes and calculates the area under the enrichment curve	KEGG	28968630
EnrichNet	Target genes are mapped to a network, and random walk procedure scores the functional associations (distance) between target and pathway genes	KEGG, BioCarta, Reactome, WikiPathways, Gene Ontolgy, NCI Pathway	22962466