Table 1 Overview of the extent of overlapping gene sets in some commonly used gene set databases
From: Avoiding the pitfalls of gene set enrichment analysis with SetRank
DB | # sets | median size | % overlap | Min. | p25 | Median | p75 | Max. |
|---|---|---|---|---|---|---|---|---|
BIOCYC | 596 | 3 | 3.4% | 1.45% | 11.61% | 20.00% | 38.46% | 100.00% |
GOBP | 14524 | 6 | 18.2% | 0.01% | 0.31% | 0.76% | 1.75% | 100.00% |
GOCC | 1751 | 7 | 15.8% | 0.01% | 0.16% | 0.49% | 1.45% | 100.00% |
GOMF | 4388 | 3 | 6.1% | 0.01% | 0.17% | 0.50% | 1.53% | 100.00% |
KEGG | 956 | 29 | 13.1% | 0.07% | 1.61% | 4.12% | 8.98% | 100.00% |
Pathway Interaction Database | 186 | 32.5 | 50.5% | 0.52% | 1.75% | 3.45% | 6.38% | 63.64% |
REACTOME | 1784 | 19 | 11.8% | 0.04% | 1.00% | 2.44% | 6.29% | 100.00% |
WikiPathways | 239 | 32 | 26.5% | 0.24% | 1.31% | 2.61% | 5.34% | 100.00% |