| Motif | RARA.H12INVIVO.2.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 2 |
| Quality | B |
| Motif | RARA.H12INVIVO.2.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 2 |
| Quality | B |
| Motif length | 17 |
| Consensus | hvAGGTCAbnnhRhhMn |
| GC content | 54.03% |
| Information content (bits; total / per base) | 10.99 / 0.646 |
| Data sources | ChIP-Seq |
| Aligned words | 1003 |
| ChIP-Seq benchmarking | Num. of experiments (peaksets) | auROC, median | auROC, best | auPRC, median | auPRC, best | pseudo-auROC, median | pseudo-auROC, best | pseudo-log-auROC, median | pseudo-log-auROC, best | Centrality, median | Centrality, best |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Human | 5 (29) | 0.731 | 0.819 | 0.54 | 0.787 | 0.694 | 0.787 | 1.702 | 3.497 | 52.77 | 135.469 |
| Mouse | 10 (46) | 0.729 | 0.832 | 0.593 | 0.709 | 0.697 | 0.786 | 1.921 | 2.383 | 53.953 | 226.678 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.763 | 0.738 | 0.743 | 0.721 | 0.713 | 0.693 |
| best | 0.96 | 0.932 | 0.946 | 0.912 | 0.9 | 0.867 | |
| Methyl HT-SELEX, 1 experiments | median | 0.96 | 0.932 | 0.944 | 0.912 | 0.9 | 0.866 |
| best | 0.96 | 0.932 | 0.944 | 0.912 | 0.9 | 0.866 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.568 | 0.548 | 0.541 | 0.531 | 0.525 | 0.521 |
| best | 0.958 | 0.928 | 0.946 | 0.912 | 0.9 | 0.867 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 1.549 | 1.628 | 0.155 | 0.046 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.599 | 0.071 | 0.459 | 0.225 |
| TF superclass | Zinc-coordinating DNA-binding domains {2} (TFClass) |
| TF class | Nuclear receptors with C4 zinc fingers {2.1} (TFClass) |
| TF family | Thyroid hormone receptor-related {2.1.2} (TFClass) |
| TF subfamily | RAR (NR1B) {2.1.2.1} (TFClass) |
| TFClass ID | TFClass: 2.1.2.1.1 |
| HGNC | HGNC:9864 |
| MGI | MGI:97856 |
| EntrezGene (human) | GeneID:5914 (SSTAR profile) |
| EntrezGene (mouse) | GeneID:19401 (SSTAR profile) |
| UniProt ID (human) | RARA_HUMAN |
| UniProt ID (mouse) | RARA_MOUSE |
| UniProt AC (human) | P10276 (TFClass) |
| UniProt AC (mouse) | P11416 (TFClass) |
| GRECO-DB-TF | yes |
| ChIP-Seq | 5 human, 10 mouse |
| HT-SELEX | 3 |
| Methyl-HT-SELEX | 1 |
| PCM | RARA.H12INVIVO.2.P.B.pcm |
| PWM | RARA.H12INVIVO.2.P.B.pwm |
| PFM | RARA.H12INVIVO.2.P.B.pfm |
| Alignment | RARA.H12INVIVO.2.P.B.words.tsv |
| Threshold to P-value map | RARA.H12INVIVO.2.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12INVIVO.2.P.B_jaspar_format.txt |
| MEME format | RARA.H12INVIVO.2.P.B_meme_format.meme |
| Transfac format | RARA.H12INVIVO.2.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 240.25 | 403.25 | 162.25 | 197.25 |
| 02 | 321.25 | 356.25 | 169.25 | 156.25 |
| 03 | 764.25 | 5.25 | 225.25 | 8.25 |
| 04 | 33.25 | 1.25 | 855.25 | 113.25 |
| 05 | 12.25 | 17.25 | 934.25 | 39.25 |
| 06 | 22.25 | 16.25 | 62.25 | 902.25 |
| 07 | 5.0 | 930.0 | 49.0 | 19.0 |
| 08 | 968.0 | 16.0 | 10.0 | 9.0 |
| 09 | 149.0 | 365.0 | 306.0 | 183.0 |
| 10 | 316.0 | 247.0 | 257.0 | 183.0 |
| 11 | 205.0 | 274.0 | 365.0 | 159.0 |
| 12 | 218.0 | 152.0 | 103.0 | 530.0 |
| 13 | 203.0 | 97.0 | 645.0 | 58.0 |
| 14 | 423.0 | 248.0 | 146.0 | 186.0 |
| 15 | 148.0 | 591.0 | 93.0 | 171.0 |
| 16 | 161.0 | 616.0 | 71.0 | 155.0 |
| 17 | 127.0 | 296.0 | 127.0 | 453.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.24 | 0.402 | 0.162 | 0.197 |
| 02 | 0.32 | 0.355 | 0.169 | 0.156 |
| 03 | 0.762 | 0.005 | 0.225 | 0.008 |
| 04 | 0.033 | 0.001 | 0.853 | 0.113 |
| 05 | 0.012 | 0.017 | 0.931 | 0.039 |
| 06 | 0.022 | 0.016 | 0.062 | 0.9 |
| 07 | 0.005 | 0.927 | 0.049 | 0.019 |
| 08 | 0.965 | 0.016 | 0.01 | 0.009 |
| 09 | 0.149 | 0.364 | 0.305 | 0.182 |
| 10 | 0.315 | 0.246 | 0.256 | 0.182 |
| 11 | 0.204 | 0.273 | 0.364 | 0.159 |
| 12 | 0.217 | 0.152 | 0.103 | 0.528 |
| 13 | 0.202 | 0.097 | 0.643 | 0.058 |
| 14 | 0.422 | 0.247 | 0.146 | 0.185 |
| 15 | 0.148 | 0.589 | 0.093 | 0.17 |
| 16 | 0.161 | 0.614 | 0.071 | 0.155 |
| 17 | 0.127 | 0.295 | 0.127 | 0.452 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | -0.042 | 0.473 | -0.432 | -0.238 |
| 02 | 0.246 | 0.349 | -0.39 | -0.469 |
| 03 | 1.11 | -3.589 | -0.106 | -3.231 |
| 04 | -1.977 | -4.44 | 1.222 | -0.787 |
| 05 | -2.894 | -2.588 | 1.31 | -1.818 |
| 06 | -2.354 | -2.642 | -1.373 | 1.275 |
| 07 | -3.625 | 1.306 | -1.605 | -2.5 |
| 08 | 1.346 | -2.656 | -3.069 | -3.158 |
| 09 | -0.516 | 0.373 | 0.198 | -0.312 |
| 10 | 0.23 | -0.015 | 0.024 | -0.312 |
| 11 | -0.2 | 0.088 | 0.373 | -0.452 |
| 12 | -0.139 | -0.496 | -0.88 | 0.745 |
| 13 | -0.21 | -0.939 | 0.941 | -1.442 |
| 14 | 0.52 | -0.011 | -0.536 | -0.296 |
| 15 | -0.523 | 0.853 | -0.98 | -0.38 |
| 16 | -0.439 | 0.895 | -1.245 | -0.477 |
| 17 | -0.674 | 0.165 | -0.674 | 0.588 |
| P-value | Threshold |
|---|---|
| 0.001 | 4.48771 |
| 0.0005 | 5.39381 |
| 0.0001 | 7.25831 |