| Motif | RARA.H12INVITRO.1.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 1 |
| Quality | B |
| Motif | RARA.H12INVITRO.1.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 1 |
| Quality | B |
| Motif length | 20 |
| Consensus | nRRGGTCAvvvvddSRdbRv |
| GC content | 54.72% |
| Information content (bits; total / per base) | 12.311 / 0.616 |
| Data sources | ChIP-Seq |
| Aligned words | 1039 |
| 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) | 0.697 | 0.846 | 0.463 | 0.679 | 0.757 | 0.875 | 2.456 | 4.383 | 41.959 | 133.328 |
| Mouse | 10 (46) | 0.772 | 0.841 | 0.671 | 0.75 | 0.762 | 0.825 | 2.574 | 3.054 | 87.143 | 260.444 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.764 | 0.746 | 0.733 | 0.715 | 0.689 | 0.674 |
| best | 0.967 | 0.948 | 0.94 | 0.913 | 0.882 | 0.853 | |
| Methyl HT-SELEX, 1 experiments | median | 0.967 | 0.948 | 0.94 | 0.913 | 0.882 | 0.853 |
| best | 0.967 | 0.948 | 0.94 | 0.913 | 0.882 | 0.853 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.565 | 0.551 | 0.538 | 0.531 | 0.523 | 0.52 |
| best | 0.962 | 0.942 | 0.927 | 0.898 | 0.855 | 0.828 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 1.68 | 2.091 | 0.125 | 0.076 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.549 | 0.048 | 0.393 | 0.21 |
| 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.H12INVITRO.1.P.B.pcm |
| PWM | RARA.H12INVITRO.1.P.B.pwm |
| PFM | RARA.H12INVITRO.1.P.B.pfm |
| Alignment | RARA.H12INVITRO.1.P.B.words.tsv |
| Threshold to P-value map | RARA.H12INVITRO.1.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12INVITRO.1.P.B_jaspar_format.txt |
| MEME format | RARA.H12INVITRO.1.P.B_meme_format.meme |
| Transfac format | RARA.H12INVITRO.1.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 305.0 | 174.0 | 181.0 | 379.0 |
| 02 | 268.0 | 73.0 | 665.0 | 33.0 |
| 03 | 668.0 | 4.0 | 359.0 | 8.0 |
| 04 | 23.0 | 2.0 | 994.0 | 20.0 |
| 05 | 7.0 | 18.0 | 816.0 | 198.0 |
| 06 | 13.0 | 29.0 | 90.0 | 907.0 |
| 07 | 18.0 | 900.0 | 100.0 | 21.0 |
| 08 | 955.0 | 32.0 | 46.0 | 6.0 |
| 09 | 289.0 | 167.0 | 447.0 | 136.0 |
| 10 | 238.0 | 186.0 | 485.0 | 130.0 |
| 11 | 420.0 | 219.0 | 251.0 | 149.0 |
| 12 | 288.0 | 107.0 | 547.0 | 97.0 |
| 13 | 205.0 | 117.0 | 373.0 | 344.0 |
| 14 | 387.0 | 58.0 | 248.0 | 346.0 |
| 15 | 48.0 | 322.0 | 637.0 | 32.0 |
| 16 | 295.0 | 31.0 | 596.0 | 117.0 |
| 17 | 374.0 | 108.0 | 196.0 | 361.0 |
| 18 | 73.0 | 499.0 | 367.0 | 100.0 |
| 19 | 761.0 | 72.0 | 142.0 | 64.0 |
| 20 | 179.0 | 418.0 | 294.0 | 148.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.294 | 0.167 | 0.174 | 0.365 |
| 02 | 0.258 | 0.07 | 0.64 | 0.032 |
| 03 | 0.643 | 0.004 | 0.346 | 0.008 |
| 04 | 0.022 | 0.002 | 0.957 | 0.019 |
| 05 | 0.007 | 0.017 | 0.785 | 0.191 |
| 06 | 0.013 | 0.028 | 0.087 | 0.873 |
| 07 | 0.017 | 0.866 | 0.096 | 0.02 |
| 08 | 0.919 | 0.031 | 0.044 | 0.006 |
| 09 | 0.278 | 0.161 | 0.43 | 0.131 |
| 10 | 0.229 | 0.179 | 0.467 | 0.125 |
| 11 | 0.404 | 0.211 | 0.242 | 0.143 |
| 12 | 0.277 | 0.103 | 0.526 | 0.093 |
| 13 | 0.197 | 0.113 | 0.359 | 0.331 |
| 14 | 0.372 | 0.056 | 0.239 | 0.333 |
| 15 | 0.046 | 0.31 | 0.613 | 0.031 |
| 16 | 0.284 | 0.03 | 0.574 | 0.113 |
| 17 | 0.36 | 0.104 | 0.189 | 0.347 |
| 18 | 0.07 | 0.48 | 0.353 | 0.096 |
| 19 | 0.732 | 0.069 | 0.137 | 0.062 |
| 20 | 0.172 | 0.402 | 0.283 | 0.142 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.16 | -0.397 | -0.358 | 0.376 |
| 02 | 0.031 | -1.252 | 0.936 | -2.019 |
| 03 | 0.941 | -3.82 | 0.322 | -3.291 |
| 04 | -2.358 | -4.248 | 1.337 | -2.487 |
| 05 | -3.399 | -2.584 | 1.14 | -0.269 |
| 06 | -2.876 | -2.141 | -1.047 | 1.246 |
| 07 | -2.584 | 1.238 | -0.944 | -2.442 |
| 08 | 1.297 | -2.048 | -1.701 | -3.52 |
| 09 | 0.106 | -0.438 | 0.54 | -0.641 |
| 10 | -0.087 | -0.331 | 0.621 | -0.686 |
| 11 | 0.478 | -0.169 | -0.034 | -0.551 |
| 12 | 0.103 | -0.877 | 0.741 | -0.974 |
| 13 | -0.235 | -0.789 | 0.36 | 0.279 |
| 14 | 0.397 | -1.476 | -0.046 | 0.285 |
| 15 | -1.66 | 0.214 | 0.893 | -2.048 |
| 16 | 0.126 | -2.078 | 0.827 | -0.789 |
| 17 | 0.363 | -0.868 | -0.279 | 0.327 |
| 18 | -1.252 | 0.65 | 0.344 | -0.944 |
| 19 | 1.071 | -1.266 | -0.598 | -1.381 |
| 20 | -0.369 | 0.473 | 0.123 | -0.558 |
| P-value | Threshold |
|---|---|
| 0.001 | 4.13366 |
| 0.0005 | 5.09451 |
| 0.0001 | 7.08696 |