Table 1. Description of the motif and track collections used.
| Source | Organism(s) | Type of motif | # motifs “6K” | # motifs “10K” | # tracks “1K ChIP” |
| Elemento [73] | Drosophila | Predicted (conserved)a | 371 | 371 | - |
| FlyFactorSurvey [75] | Drosophila | B-1H, others (e.g., FlyReg) | 614 | 652 | - |
| hPDI [77] | Human | Experimental | 437 | 437 | - |
| Jaspar [21] | Multiple species | Curated | 1315 | 1315 | - |
| SelexConsensus [76] | Drosophila | Curated (FlyReg) | 38 | 38 | - |
| Stark [74] | Drosophila | Predicted (conserved)a | 228 | 228 | - |
| Tiffin [76] | Drosophila | Predicted (gene sets)a | 120 | 120 | - |
| TRANSFAC PUBLIC [5] | Multiple species | Curated, ChIP-chip | 398 | 398 | - |
| TRANSFAC PRO [5] | Multiple species | Curated, ChIP-chip | 1153 | 1850 | - |
| YetFasco [78] | Yeast | Uniprobe, Curated, ChIP-chip | 1709 | 1709 | - |
| ENCODE [79] | Human | Predicted (from DHS)a | - | 683 | - |
| Factorbook [46] | Human | ENCODE ChIP-Seq motifs | - | 79 | - |
| Taipale [132] | Human, Mouse | HT-Selex | - | 820 | - |
| iDMMPMM [133] | Human | footprints, Selex, b1h, peaks | - | 39 | - |
| SwissRegulon [134] | Human | Curated | - | 190 | - |
| Wolfe [135] | Drosophila | ZFP motifs | - | 36 | - |
| HOMER [116] | Multiple species | ChIP-Seq Motifs, others (e.g. ENCODE) | - | 1865 | - |
| Dimers [136] | Human | Predicted dimers | - | 603 | - |
| ENCODE ChIP-Seq [23] | Human | - | - | - | 999 |
| Taipale ChIP-Seq [24] | Human | - | - | - | 117 |
| p53 and control ChIP-Seq (this study) | Human | - | - | - | 2 |
| Total | 6383 | 11611 (9713 nr) | 1118 |
a
Orphan motifs (unknown TFs).
nr = non-redundant.