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Table 1 Summary of seven enrichment methods evaluated in this study

From: Comparative study on gene set and pathway topology-based enrichment methods

Test/Method name Pathway representation ORA/ FCS R-function/ package version Database support Null hypothesis
Wilcoxon rank sum GS FCS wilcox.test Any input Competitive
Kolmogorov-Smirnov GS FCS ks.test Any input Competitive
Fisher’s exact GS ORA fisher.test Any input Competitive
SPIA PT-based ORA-like 2.12.0. KEGG Competitive
CePa ORA PT-based ORA-like 0.5. KEGG, Reactome, NCI-Nature, BioCarta Competitive
CePa GSA PT-based FCS-like 0.5. Self-contained
PathNet PT-based unclass. 1.3.0. KEGG Competitive
  1. Methods were classified according to the representation of a pathway into the gene set (GS) enrichment and the pathway topology-based (PT-based) methods. Second column stratifies the methods into over-representation analysis (ORA) and functional class scoring (FCS). However, for PT-based methods this classification is not always explicit, therefore we used ‘-like’ suffix and ‘unclass.’ for an unclassified method. Third column shows the utilized R-functions for GS methods and versions of R-packages of PT-based methods. Next column summarizes the pathways databases which are provided within the R-packages. According to the null hypothesis most of the methods are competitive, only the GSA variant of the CePa method is self-contained