Table 3.
Enrichment of ENCODE transcription factor measured binding
| Enrichments of ENCODE transcription factor binding |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| AP-2 alpha | AP-2 gamma | c-Jun | JunD | SP1 | STAT1 | CTCF | BAF155 | GR | BCL3 | |
| SP1 var | 106 | 96 | 34 | 35 | 56 | 65 | 11 | 155 | 84 | 61 |
| Gapped SP1 | 68 | 64 | 42 | 39 | 38 | 60 | 7 | 91 | 74 | 41 |
| Long gapped SP1 | 77 | 71 | 38 | 36 | 46 | 59 | 10 | 122 | 79 | 45 |
| AP1 | 94 | 90 | 97 | 100 | 43 | 82 | 5 | 154 | 125 | 56 |
Selected ENCODE transcription factors and four de novo motifs (three dominant variants of SP1 motif and AP1 motif) are shown, full list is available on Supplementary webpage. Note that binding of AP1 subunits, as measured by ENCODE consortium, is especially enriched in location where we detect AP1 sequence motifs. Moreover, RelA ChIP-Seq peaks exhibit different enrichments of binding of many TFs examined by ENCODE, depending on the presence of SP1 motifs or AP1 motif. For some transcription factors, SP1 motifs with middle ‘T’ (gapped SP1 and long gapped SP1) exhibit different co-occurrence preferences than SP1 var motif.