| Motif | VDR.H12INVIVO.1.PS.A |
| Gene (human) | VDR (GeneCards) |
| Gene synonyms (human) | NR1I1 |
| Gene (mouse) | Vdr |
| Gene synonyms (mouse) | Nr1i1 |
| LOGO |  |
| LOGO (reverse complement) |  |
| Motif subtype | 1 |
| Quality | A |
| Motif | VDR.H12INVIVO.1.PS.A |
| Gene (human) | VDR (GeneCards) |
| Gene synonyms (human) | NR1I1 |
| Gene (mouse) | Vdr |
| Gene synonyms (mouse) | Nr1i1 |
| LOGO | |
| LOGO (reverse complement) | |
| Motif subtype | 1 |
| Quality | A |
| Motif length | 9 |
| Consensus | hRGGTTCAb |
| GC content | 51.59% |
| Information content (bits; total / per base) | 10.449 / 1.161 |
| Data sources | ChIP-Seq + HT-SELEX |
| Aligned words | 1000 |
| 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 | 45 (197) | 0.705 | 0.897 | 0.551 | 0.829 | 0.678 | 0.87 | 1.76 | 3.245 | 66.387 | 444.796 |
| Mouse | 10 (52) | 0.717 | 0.824 | 0.589 | 0.697 | 0.68 | 0.788 | 1.785 | 2.169 | 79.808 | 147.721 |
| HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
|---|---|---|---|---|---|---|---|
| Non-Methyl HT-SELEX, 4 experiments | median | 0.742 | 0.718 | 0.642 | 0.635 | 0.575 | 0.583 |
| best | 0.984 | 0.975 | 0.946 | 0.932 | 0.807 | 0.813 | |
| 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 | VDR (NR1I) {2.1.2.4} (TFClass) |
| TFClass ID | TFClass: 2.1.2.4.1 |
| HGNC | HGNC:12679 |
| MGI | MGI:103076 |
| EntrezGene (human) | GeneID:7421 (SSTAR profile) |
| EntrezGene (mouse) | GeneID:22337 (SSTAR profile) |
| UniProt ID (human) | VDR_HUMAN |
| UniProt ID (mouse) | VDR_MOUSE |
| UniProt AC (human) | P11473 (TFClass) |
| UniProt AC (mouse) | P48281 (TFClass) |
| GRECO-DB-TF | yes |
| ChIP-Seq | 45 human, 10 mouse |
| HT-SELEX | 4 |
| Methyl-HT-SELEX | 0 |
| PCM | VDR.H12INVIVO.1.PS.A.pcm |
| PWM | VDR.H12INVIVO.1.PS.A.pwm |
| PFM | VDR.H12INVIVO.1.PS.A.pfm |
| Alignment | VDR.H12INVIVO.1.PS.A.words.tsv |
| Threshold to P-value map | VDR.H12INVIVO.1.PS.A.thr |
| Motif in other formats | |
| JASPAR format | VDR.H12INVIVO.1.PS.A_jaspar_format.txt |
| MEME format | VDR.H12INVIVO.1.PS.A_meme_format.meme |
| Transfac format | VDR.H12INVIVO.1.PS.A_transfac_format.txt |
| Homer format | |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 265.0 | 292.0 | 102.0 | 341.0 |
| 02 | 222.0 | 16.0 | 740.0 | 22.0 |
| 03 | 298.0 | 0.0 | 699.0 | 3.0 |
| 04 | 1.0 | 0.0 | 998.0 | 1.0 |
| 05 | 3.0 | 4.0 | 307.0 | 686.0 |
| 06 | 6.0 | 10.0 | 41.0 | 943.0 |
| 07 | 5.0 | 964.0 | 4.0 | 27.0 |
| 08 | 971.0 | 12.0 | 10.0 | 7.0 |
| 09 | 136.0 | 230.0 | 214.0 | 420.0 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.265 | 0.292 | 0.102 | 0.341 |
| 02 | 0.222 | 0.016 | 0.74 | 0.022 |
| 03 | 0.298 | 0.0 | 0.699 | 0.003 |
| 04 | 0.001 | 0.0 | 0.998 | 0.001 |
| 05 | 0.003 | 0.004 | 0.307 | 0.686 |
| 06 | 0.006 | 0.01 | 0.041 | 0.943 |
| 07 | 0.005 | 0.964 | 0.004 | 0.027 |
| 08 | 0.971 | 0.012 | 0.01 | 0.007 |
| 09 | 0.136 | 0.23 | 0.214 | 0.42 |
| A | C | G | T | |
|---|---|---|---|---|
| 01 | 0.058 | 0.154 | -0.887 | 0.309 |
| 02 | -0.118 | -2.653 | 1.081 | -2.362 |
| 03 | 0.175 | -4.982 | 1.024 | -3.975 |
| 04 | -4.525 | -4.982 | 1.379 | -4.525 |
| 05 | -3.975 | -3.783 | 0.204 | 1.005 |
| 06 | -3.484 | -3.066 | -1.774 | 1.323 |
| 07 | -3.622 | 1.345 | -3.783 | -2.171 |
| 08 | 1.352 | -2.909 | -3.066 | -3.362 |
| 09 | -0.603 | -0.083 | -0.154 | 0.516 |
| P-value | Threshold |
|---|---|
| 0.001 | 4.28091 |
| 0.0005 | 5.43377 |
| 0.0001 | 7.75858 |