Table 2 Benchmarking results for SetRank compared to other methods
From: Avoiding the pitfalls of gene set enrichment analysis with SetRank
Method | Sensitivity | Prioritization | Specificity |
|---|---|---|---|
PLAGE [28] | 0.0022 | 25.00% | 1.10% |
GLOBALTEST [29] | 0.0001 | 27.90% | 2.00% |
PADOG [7] | 0.096 | 9.70% | 2.50% |
ORA | 0.0732 | 18.30% | 2.50% |
SAFE [30] | 0.1065 | 18.80% | 1.30% |
SIGPATHWAY Q2 [31] | 0.0565 | 38.00% | 0.90% |
GSA [32] | 0.142 | 21.00% | 1.30% |
SSGSEA [33] | 0.0808 | 40.30% | 1.00% |
ZSCORE [34] | 0.095 | 39.80% | 1.00% |
GSEA [35] | 0.1801 | 33.10% | 2.30% |
GSVA [36] | 0.1986 | 51.50% | 1.10% |
CAMERA [37] | 0.3126 | 43.00% | 0.50% |
MRGSE [38] | 0.01 | 18.80% | 4.90% |
GSEAP | 0.0644 | 36.20% | 15.80% |
GAGE [39] | 0.0024 | 35.90% | 37.90% |
SIGPATHWAY. Q1 | 0.1165 | 49.70% | 17.20% |
SetRank filtered | 1.0 | 0.75% (10) | 0.09% |
no filter | 1.0 | 2.05% (10) | – |