Table 2.
Summary of tools benchmarked against ChEA3
| Tool | TF coveragea | Required input | Method | Data used to make predictions | Availability |
|---|---|---|---|---|---|
| TFEA.ChIP (9) | 271 | Gene set or sorted list of DEGs | FET or GSEA (15) | ENCODE (22) and GEO (19) ChIP-seq experiments | R package, Web Server https://www.iib.uam.es/TFEA.ChIP/ |
| BART (8) | 273 | Gene set | Correlates cis-regulatory profile derived from query gene set with TF genomic binding profiles | DNAse I hypersensitivity, TF ChIP-seq | Standalone Application, Web Server http://bartweb.uvasomrc.io |
| VIPER (5) | 454b, 731c, 1,607d | Gene signature | aREA (analytic Rank-based Enrichment Analysis) (5) | ARACNe-generated gene regulatory network in same tissue type as query | R package |
| DoRothEA v2 (7) | Reg. A: 163 Reg. B: 188 Reg. C: 313 Reg. D: 416 Reg. E: 1306 Top10Score: 1306 | Gene signature | aREA (5) | Literature, ReMap ChIP-seq (26), TF motif (47,48), GTEx co-expression (12) | R object for use with VIPER R package |
| MAGICACT (11) | 109 | Gene set | Mann-Whitney test | ENCODE (22) ChIP-seq | Standalone Application |
aHGNC-mappable TFs that are considered site-specific TFs as defined by Lambert (1). Some tools contain additional general transcription factors, co-factors, or chromatin modifiers.
bPublished B-cell regulatory network available in the bcellviper R package.
dARACNe-AP built network using expression data from GTEx (12).