| Motif | RARA.H12INVITRO.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.H12INVITRO.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 | vdbbvdRAGKTCARRRhSRbb |
| GC content | 53.08% |
| Information content (bits; total / per base) | 14.199 / 0.676 |
| Data sources | ChIP-Seq |
| Aligned words | 989 |
| 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) | 0.689 | 0.771 | 0.484 | 0.62 | 0.717 | 0.807 | 2.155 | 3.29 | 30.301 | 141.229 |
| Mouse | 10 (46) | 0.814 | 0.913 | 0.741 | 0.882 | 0.83 | 0.921 | 5.196 | 8.001 | 112.67 | 473.252 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Overall, 4 experiments | median | 0.757 | 0.741 | 0.727 | 0.711 | 0.69 | 0.675 |
| best | 0.96 | 0.936 | 0.935 | 0.903 | 0.881 | 0.848 | |
| Methyl HT-SELEX, 1 experiments | median | 0.959 | 0.935 | 0.927 | 0.896 | 0.868 | 0.835 |
| best | 0.959 | 0.935 | 0.927 | 0.896 | 0.868 | 0.835 | |
| Non-Methyl HT-SELEX, 3 experiments | median | 0.556 | 0.547 | 0.527 | 0.526 | 0.511 | 0.515 |
| best | 0.96 | 0.936 | 0.935 | 0.903 | 0.881 | 0.848 | |
| rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
|---|---|---|---|---|
| # | 2.69 | 6.143 | 0.177 | 0.105 |
| rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
|---|---|---|---|---|
| batch 2 | 0.594 | 0.059 | 0.496 | 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.H12INVITRO.3.P.B.pcm |
| PWM | RARA.H12INVITRO.3.P.B.pwm |
| PFM | RARA.H12INVITRO.3.P.B.pfm |
| Alignment | RARA.H12INVITRO.3.P.B.words.tsv |
| Threshold to P-value map | RARA.H12INVITRO.3.P.B.thr |
| Motif in other formats | |
| JASPAR format | RARA.H12INVITRO.3.P.B_jaspar_format.txt |
| MEME format | RARA.H12INVITRO.3.P.B_meme_format.meme |
| Transfac format | RARA.H12INVITRO.3.P.B_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 180.0 | 150.0 | 544.0 | 115.0 |
| 02 | 261.0 | 112.0 | 421.0 | 195.0 |
| 03 | 116.0 | 182.0 | 206.0 | 485.0 |
| 04 | 127.0 | 513.0 | 206.0 | 143.0 |
| 05 | 494.0 | 230.0 | 179.0 | 86.0 |
| 06 | 425.0 | 81.0 | 313.0 | 170.0 |
| 07 | 370.0 | 55.0 | 536.0 | 28.0 |
| 08 | 739.0 | 7.0 | 226.0 | 17.0 |
| 09 | 23.0 | 11.0 | 938.0 | 17.0 |
| 10 | 6.0 | 10.0 | 480.0 | 493.0 |
| 11 | 9.0 | 40.0 | 38.0 | 902.0 |
| 12 | 13.0 | 919.0 | 48.0 | 9.0 |
| 13 | 965.0 | 7.0 | 11.0 | 6.0 |
| 14 | 683.0 | 45.0 | 211.0 | 50.0 |
| 15 | 164.0 | 67.0 | 724.0 | 34.0 |
| 16 | 106.0 | 79.0 | 706.0 | 98.0 |
| 17 | 163.0 | 209.0 | 157.0 | 460.0 |
| 18 | 81.0 | 596.0 | 188.0 | 124.0 |
| 19 | 651.0 | 47.0 | 183.0 | 108.0 |
| 20 | 122.0 | 132.0 | 508.0 | 227.0 |
| 21 | 103.0 | 339.0 | 371.0 | 176.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.182 | 0.152 | 0.55 | 0.116 |
| 02 | 0.264 | 0.113 | 0.426 | 0.197 |
| 03 | 0.117 | 0.184 | 0.208 | 0.49 |
| 04 | 0.128 | 0.519 | 0.208 | 0.145 |
| 05 | 0.499 | 0.233 | 0.181 | 0.087 |
| 06 | 0.43 | 0.082 | 0.316 | 0.172 |
| 07 | 0.374 | 0.056 | 0.542 | 0.028 |
| 08 | 0.747 | 0.007 | 0.229 | 0.017 |
| 09 | 0.023 | 0.011 | 0.948 | 0.017 |
| 10 | 0.006 | 0.01 | 0.485 | 0.498 |
| 11 | 0.009 | 0.04 | 0.038 | 0.912 |
| 12 | 0.013 | 0.929 | 0.049 | 0.009 |
| 13 | 0.976 | 0.007 | 0.011 | 0.006 |
| 14 | 0.691 | 0.046 | 0.213 | 0.051 |
| 15 | 0.166 | 0.068 | 0.732 | 0.034 |
| 16 | 0.107 | 0.08 | 0.714 | 0.099 |
| 17 | 0.165 | 0.211 | 0.159 | 0.465 |
| 18 | 0.082 | 0.603 | 0.19 | 0.125 |
| 19 | 0.658 | 0.048 | 0.185 | 0.109 |
| 20 | 0.123 | 0.133 | 0.514 | 0.23 |
| 21 | 0.104 | 0.343 | 0.375 | 0.178 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | -0.315 | -0.495 | 0.785 | -0.758 |
| 02 | 0.054 | -0.784 | 0.529 | -0.236 |
| 03 | -0.749 | -0.304 | -0.181 | 0.67 |
| 04 | -0.66 | 0.726 | -0.181 | -0.543 |
| 05 | 0.689 | -0.072 | -0.32 | -1.043 |
| 06 | 0.539 | -1.102 | 0.234 | -0.371 |
| 07 | 0.401 | -1.479 | 0.77 | -2.125 |
| 08 | 1.09 | -3.351 | -0.089 | -2.588 |
| 09 | -2.31 | -2.974 | 1.328 | -2.588 |
| 10 | -3.473 | -3.056 | 0.66 | 0.687 |
| 11 | -3.145 | -1.786 | -1.835 | 1.289 |
| 12 | -2.828 | 1.308 | -1.611 | -3.145 |
| 13 | 1.357 | -3.351 | -2.974 | -3.473 |
| 14 | 1.012 | -1.673 | -0.157 | -1.571 |
| 15 | -0.407 | -1.287 | 1.07 | -1.942 |
| 16 | -0.838 | -1.126 | 1.045 | -0.915 |
| 17 | -0.413 | -0.167 | -0.45 | 0.618 |
| 18 | -1.102 | 0.876 | -0.272 | -0.683 |
| 19 | 0.964 | -1.631 | -0.298 | -0.819 |
| 20 | -0.699 | -0.622 | 0.717 | -0.085 |
| 21 | -0.866 | 0.314 | 0.403 | -0.337 |
| P-value | Threshold |
|---|---|
| 0.001 | 3.53111 |
| 0.0005 | 4.58246 |
| 0.0001 | 6.78261 |