TREs enriched in Socs3 h-KO mice 18 h after PH
| Candidate binding factor for TRE . | TRE consensus sequence . | Counts . | p-value . |
|---|---|---|---|
| NF-κB superfamily | |||
| c-Rel | SGGRNTTTCC | 87 | 0.05 |
| NF-κB | NGGGGAMTTTCCNN | 20 | 0.25 |
| NF-κB | GGGAMTTYCC | 15 | 0.02 |
| NF-κB (p65) | GGGRATTTCC | 12 | 0.01 |
| Cell growth and proliferation | |||
| Elk-1 | NAAACMGGAAGTNCVH | 71 | 0.02 |
| c-Jun/CRE-BP1 | TGACGTYA | 42 | 0.28 |
| CREB | TGACGTMA | 39 | 0.09 |
| Evi-1 | WGAYAAGATAGATAA | 25 | 0.19 |
| E2F | TTTSGCGC | 20 | 0.04 |
| ATF-2/CRE-BP1 | VGTGACGTMACN | 14 | 0.28 |
| CREB | NSTGACGTAANN | 11 | 0.07 |
| Egr-1 | WTGCGTGGGCGK | 1 | 0.39 |
| Egr-3 | NTGCGTGGGCGK | 1 | 0.28 |
| Differentiation and hepatocyte specificity | |||
| USF | GYCACGTGNC | 49 | 0.09 |
| Pax-6 | NNNNTTCACGCWTGANTKNNN | 34 | 0.28 |
| USF | NCACGTGN | 31 | 0.28 |
| CP2 | GCHCDAMCCAG | 23 | 0.17 |
| Oct-1 | CWNAWTKWSATRYN | 22 | 0.28 |
| HNF-4/COUP-TF | TGAMCTTTGMMCYT | 12 | 0.05 |
| Oct-1 | MKVATTTGCATATT | 7 | 0.41 |
| MEF-2 | NNTGTTACTAAAAATAGAAMNN | 2 | 0.21 |
| Candidate binding factor for TRE . | TRE consensus sequence . | Counts . | p-value . |
|---|---|---|---|
| NF-κB superfamily | |||
| c-Rel | SGGRNTTTCC | 87 | 0.05 |
| NF-κB | NGGGGAMTTTCCNN | 20 | 0.25 |
| NF-κB | GGGAMTTYCC | 15 | 0.02 |
| NF-κB (p65) | GGGRATTTCC | 12 | 0.01 |
| Cell growth and proliferation | |||
| Elk-1 | NAAACMGGAAGTNCVH | 71 | 0.02 |
| c-Jun/CRE-BP1 | TGACGTYA | 42 | 0.28 |
| CREB | TGACGTMA | 39 | 0.09 |
| Evi-1 | WGAYAAGATAGATAA | 25 | 0.19 |
| E2F | TTTSGCGC | 20 | 0.04 |
| ATF-2/CRE-BP1 | VGTGACGTMACN | 14 | 0.28 |
| CREB | NSTGACGTAANN | 11 | 0.07 |
| Egr-1 | WTGCGTGGGCGK | 1 | 0.39 |
| Egr-3 | NTGCGTGGGCGK | 1 | 0.28 |
| Differentiation and hepatocyte specificity | |||
| USF | GYCACGTGNC | 49 | 0.09 |
| Pax-6 | NNNNTTCACGCWTGANTKNNN | 34 | 0.28 |
| USF | NCACGTGN | 31 | 0.28 |
| CP2 | GCHCDAMCCAG | 23 | 0.17 |
| Oct-1 | CWNAWTKWSATRYN | 22 | 0.28 |
| HNF-4/COUP-TF | TGAMCTTTGMMCYT | 12 | 0.05 |
| Oct-1 | MKVATTTGCATATT | 7 | 0.41 |
| MEF-2 | NNTGTTACTAAAAATAGAAMNN | 2 | 0.21 |
Enriched TREs (biologically relevant transcription factor binding sites) were identified by comparing promoter regions of genes up-regulated >1.5-fold in Socs3 h-KO mice to all M. musculus promoter regions in the PAINT database. To identify TREs overrepresented, 5 kb of upstream sequence of each gene from the list of significantly up-regulated genes was analyzed by PAINT. TRE consensus sequence is the consensus binding site for the indicated binding factor (known transcription factor), provided as the International Union of Pure and Applied Chemistry 15-letter code. Multiple listings of candidate binding factors are based on differences in consensus binding sites. Count refers to the total number of times the TRE was found in the gene set. p-values were calculated as described in Materials and methods.