| Motif | RARA.H12INVIVO.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.H12INVIVO.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 | vdbvvdRAGKTCARRRhSRdb |
| GC content | 53.35% |
| Information content (bits; total / per base) | 14.146 / 0.674 |
| Data sources | ChIP-Seq |
| Aligned words | 944 |
| 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) | 0.684 | 0.765 | 0.48 | 0.62 | 0.72 | 0.806 | 2.179 | 3.346 | 28.495 | 147.721 |
| Mouse | 10 (46) | 0.817 | 0.911 | 0.744 | 0.884 | 0.833 | 0.918 | 5.173 | 8.001 | 112.956 | 473.456 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.759 | 0.742 | 0.726 | 0.711 | 0.688 | 0.674 |
| best | 0.961 | 0.937 | 0.933 | 0.902 | 0.877 | 0.845 | |
| Methyl HT-SELEX, 1 experiments | median | 0.959 | 0.937 | 0.927 | 0.896 | 0.865 | 0.834 |
| best | 0.959 | 0.937 | 0.927 | 0.896 | 0.865 | 0.834 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.558 | 0.547 | 0.526 | 0.526 | 0.51 | 0.514 |
| best | 0.961 | 0.937 | 0.933 | 0.902 | 0.877 | 0.845 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 2.911 | 6.945 | 0.19 | 0.111 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.582 | 0.064 | 0.459 | 0.221 |
| 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.3.P.B.pcm |
| PWM | RARA.H12INVIVO.3.P.B.pwm |
| PFM | RARA.H12INVIVO.3.P.B.pfm |
| Alignment | RARA.H12INVIVO.3.P.B.words.tsv |
| Threshold to P-value map | RARA.H12INVIVO.3.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12INVIVO.3.P.B_jaspar_format.txt |
| MEME format | RARA.H12INVIVO.3.P.B_meme_format.meme |
| Transfac format | RARA.H12INVIVO.3.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 152.0 | 163.0 | 551.0 | 78.0 |
| 02 | 277.0 | 88.0 | 440.0 | 139.0 |
| 03 | 110.0 | 149.0 | 202.0 | 483.0 |
| 04 | 125.0 | 538.0 | 165.0 | 116.0 |
| 05 | 494.0 | 199.0 | 156.0 | 95.0 |
| 06 | 367.0 | 86.0 | 363.0 | 128.0 |
| 07 | 380.0 | 42.0 | 492.0 | 30.0 |
| 08 | 723.0 | 4.0 | 215.0 | 2.0 |
| 09 | 45.0 | 9.0 | 883.0 | 7.0 |
| 10 | 10.0 | 6.0 | 480.0 | 448.0 |
| 11 | 27.0 | 33.0 | 48.0 | 836.0 |
| 12 | 20.0 | 863.0 | 49.0 | 12.0 |
| 13 | 916.0 | 13.0 | 12.0 | 3.0 |
| 14 | 615.0 | 76.0 | 198.0 | 55.0 |
| 15 | 167.0 | 77.0 | 649.0 | 51.0 |
| 16 | 87.0 | 85.0 | 687.0 | 85.0 |
| 17 | 173.0 | 189.0 | 134.0 | 448.0 |
| 18 | 95.0 | 563.0 | 189.0 | 97.0 |
| 19 | 635.0 | 45.0 | 153.0 | 111.0 |
| 20 | 117.0 | 114.0 | 500.0 | 213.0 |
| 21 | 103.0 | 308.0 | 361.0 | 172.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.161 | 0.173 | 0.584 | 0.083 |
| 02 | 0.293 | 0.093 | 0.466 | 0.147 |
| 03 | 0.117 | 0.158 | 0.214 | 0.512 |
| 04 | 0.132 | 0.57 | 0.175 | 0.123 |
| 05 | 0.523 | 0.211 | 0.165 | 0.101 |
| 06 | 0.389 | 0.091 | 0.385 | 0.136 |
| 07 | 0.403 | 0.044 | 0.521 | 0.032 |
| 08 | 0.766 | 0.004 | 0.228 | 0.002 |
| 09 | 0.048 | 0.01 | 0.935 | 0.007 |
| 10 | 0.011 | 0.006 | 0.508 | 0.475 |
| 11 | 0.029 | 0.035 | 0.051 | 0.886 |
| 12 | 0.021 | 0.914 | 0.052 | 0.013 |
| 13 | 0.97 | 0.014 | 0.013 | 0.003 |
| 14 | 0.651 | 0.081 | 0.21 | 0.058 |
| 15 | 0.177 | 0.082 | 0.688 | 0.054 |
| 16 | 0.092 | 0.09 | 0.728 | 0.09 |
| 17 | 0.183 | 0.2 | 0.142 | 0.475 |
| 18 | 0.101 | 0.596 | 0.2 | 0.103 |
| 19 | 0.673 | 0.048 | 0.162 | 0.118 |
| 20 | 0.124 | 0.121 | 0.53 | 0.226 |
| 21 | 0.109 | 0.326 | 0.382 | 0.182 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | -0.436 | -0.367 | 0.844 | -1.093 |
| 02 | 0.159 | -0.974 | 0.62 | -0.524 |
| 03 | -0.755 | -0.456 | -0.154 | 0.712 |
| 04 | -0.629 | 0.82 | -0.355 | -0.703 |
| 05 | 0.735 | -0.169 | -0.41 | -0.899 |
| 06 | 0.439 | -0.997 | 0.428 | -0.606 |
| 07 | 0.474 | -1.693 | 0.731 | -2.014 |
| 08 | 1.115 | -3.728 | -0.092 | -4.159 |
| 09 | -1.627 | -3.1 | 1.314 | -3.306 |
| 10 | -3.01 | -3.428 | 0.706 | 0.638 |
| 11 | -2.114 | -1.924 | -1.565 | 1.26 |
| 12 | -2.393 | 1.291 | -1.545 | -2.853 |
| 13 | 1.351 | -2.782 | -2.853 | -3.921 |
| 14 | 0.953 | -1.118 | -0.174 | -1.433 |
| 15 | -0.343 | -1.105 | 1.007 | -1.506 |
| 16 | -0.986 | -1.008 | 1.064 | -1.008 |
| 17 | -0.308 | -0.22 | -0.561 | 0.638 |
| 18 | -0.899 | 0.865 | -0.22 | -0.879 |
| 19 | 0.985 | -1.627 | -0.429 | -0.746 |
| 20 | -0.694 | -0.72 | 0.747 | -0.102 |
| 21 | -0.82 | 0.265 | 0.423 | -0.314 |
| P-value | Threshold |
|---|---|
| 0.001 | 3.59561 |
| 0.0005 | 4.63096 |
| 0.0001 | 6.79571 |