| Motif | RARA.H12RSNP.3.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 3 |
| Quality | B |
| Motif | RARA.H12RSNP.3.P.B |
| Gene (human) | RARA (GeneCards) |
| Gene synonyms (human) | NR1B1 |
| Gene (mouse) | Rara |
| Gene synonyms (mouse) | Nr1b1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 3 |
| Quality | B |
| Motif length | 21 |
| Consensus | dbbvdRAGKTCARRRbSRbbb |
| GC content | 52.77% |
| Information content (bits; total / per base) | 14.262 / 0.679 |
| Data sources | ChIP-Seq |
| Aligned words | 993 |
| 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) | 0.686 | 0.77 | 0.486 | 0.61 | 0.703 | 0.797 | 2.066 | 3.084 | 31.387 | 144.569 |
| Mouse | 10 (46) | 0.803 | 0.909 | 0.724 | 0.874 | 0.821 | 0.918 | 5.118 | 7.843 | 102.79 | 454.509 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.756 | 0.737 | 0.727 | 0.708 | 0.69 | 0.673 |
| best | 0.956 | 0.93 | 0.929 | 0.896 | 0.871 | 0.838 | |
| Methyl HT-SELEX, 1 experiments | median | 0.955 | 0.929 | 0.924 | 0.891 | 0.865 | 0.831 |
| best | 0.955 | 0.929 | 0.924 | 0.891 | 0.865 | 0.831 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.557 | 0.545 | 0.529 | 0.526 | 0.514 | 0.515 |
| best | 0.956 | 0.93 | 0.929 | 0.896 | 0.871 | 0.838 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 2.66 | 6.127 | 0.181 | 0.1 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.655 | 0.068 | 0.502 | 0.27 |
| 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.H12RSNP.3.P.B.pcm |
| PWM | RARA.H12RSNP.3.P.B.pwm |
| PFM | RARA.H12RSNP.3.P.B.pfm |
| Alignment | RARA.H12RSNP.3.P.B.words.tsv |
| Threshold to P-value map | RARA.H12RSNP.3.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12RSNP.3.P.B_jaspar_format.txt |
| MEME format | RARA.H12RSNP.3.P.B_meme_format.meme |
| Transfac format | RARA.H12RSNP.3.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 278.0 | 115.0 | 409.0 | 191.0 |
| 02 | 100.0 | 200.0 | 231.0 | 462.0 |
| 03 | 144.0 | 517.0 | 175.0 | 157.0 |
| 04 | 464.0 | 235.0 | 194.0 | 100.0 |
| 05 | 408.0 | 79.0 | 330.0 | 176.0 |
| 06 | 390.0 | 56.0 | 518.0 | 29.0 |
| 07 | 747.0 | 8.0 | 227.0 | 11.0 |
| 08 | 15.0 | 7.0 | 955.0 | 16.0 |
| 09 | 7.0 | 10.0 | 479.0 | 497.0 |
| 10 | 6.0 | 38.0 | 46.0 | 903.0 |
| 11 | 19.0 | 915.0 | 48.0 | 11.0 |
| 12 | 967.0 | 11.0 | 10.0 | 5.0 |
| 13 | 712.0 | 43.0 | 185.0 | 53.0 |
| 14 | 143.0 | 56.0 | 760.0 | 34.0 |
| 15 | 100.0 | 75.0 | 736.0 | 82.0 |
| 16 | 137.0 | 226.0 | 146.0 | 484.0 |
| 17 | 77.0 | 618.0 | 173.0 | 125.0 |
| 18 | 663.0 | 48.0 | 157.0 | 125.0 |
| 19 | 121.0 | 145.0 | 509.0 | 218.0 |
| 20 | 107.0 | 336.0 | 372.0 | 178.0 |
| 21 | 123.0 | 423.0 | 183.0 | 264.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.28 | 0.116 | 0.412 | 0.192 |
| 02 | 0.101 | 0.201 | 0.233 | 0.465 |
| 03 | 0.145 | 0.521 | 0.176 | 0.158 |
| 04 | 0.467 | 0.237 | 0.195 | 0.101 |
| 05 | 0.411 | 0.08 | 0.332 | 0.177 |
| 06 | 0.393 | 0.056 | 0.522 | 0.029 |
| 07 | 0.752 | 0.008 | 0.229 | 0.011 |
| 08 | 0.015 | 0.007 | 0.962 | 0.016 |
| 09 | 0.007 | 0.01 | 0.482 | 0.501 |
| 10 | 0.006 | 0.038 | 0.046 | 0.909 |
| 11 | 0.019 | 0.921 | 0.048 | 0.011 |
| 12 | 0.974 | 0.011 | 0.01 | 0.005 |
| 13 | 0.717 | 0.043 | 0.186 | 0.053 |
| 14 | 0.144 | 0.056 | 0.765 | 0.034 |
| 15 | 0.101 | 0.076 | 0.741 | 0.083 |
| 16 | 0.138 | 0.228 | 0.147 | 0.487 |
| 17 | 0.078 | 0.622 | 0.174 | 0.126 |
| 18 | 0.668 | 0.048 | 0.158 | 0.126 |
| 19 | 0.122 | 0.146 | 0.513 | 0.22 |
| 20 | 0.108 | 0.338 | 0.375 | 0.179 |
| 21 | 0.124 | 0.426 | 0.184 | 0.266 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.112 | -0.762 | 0.497 | -0.26 |
| 02 | -0.899 | -0.214 | -0.072 | 0.618 |
| 03 | -0.54 | 0.73 | -0.347 | -0.454 |
| 04 | 0.622 | -0.054 | -0.245 | -0.899 |
| 05 | 0.494 | -1.13 | 0.283 | -0.341 |
| 06 | 0.449 | -1.466 | 0.732 | -2.096 |
| 07 | 1.097 | -3.247 | -0.089 | -2.978 |
| 08 | -2.704 | -3.355 | 1.342 | -2.646 |
| 09 | -3.355 | -3.06 | 0.654 | 0.691 |
| 10 | -3.477 | -1.839 | -1.656 | 1.286 |
| 11 | -2.49 | 1.299 | -1.615 | -2.978 |
| 12 | 1.355 | -2.978 | -3.06 | -3.616 |
| 13 | 1.049 | -1.721 | -0.292 | -1.519 |
| 14 | -0.547 | -1.466 | 1.114 | -1.946 |
| 15 | -0.899 | -1.181 | 1.082 | -1.094 |
| 16 | -0.589 | -0.093 | -0.526 | 0.664 |
| 17 | -1.155 | 0.908 | -0.358 | -0.679 |
| 18 | 0.978 | -1.615 | -0.454 | -0.679 |
| 19 | -0.711 | -0.533 | 0.714 | -0.129 |
| 20 | -0.833 | 0.301 | 0.402 | -0.33 |
| 21 | -0.695 | 0.53 | -0.302 | 0.061 |
| P-value | Threshold |
|---|---|
| 0.001 | 3.49386 |
| 0.0005 | 4.55341 |
| 0.0001 | 6.76991 |