Motif | PDX1.H12CORE.0.P.B |
Gene (human) | PDX1 (GeneCards) |
Gene synonyms (human) | IPF1, STF1 |
Gene (mouse) | Pdx1 |
Gene synonyms (mouse) | Ipf1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | B |
Motif | PDX1.H12CORE.0.P.B |
Gene (human) | PDX1 (GeneCards) |
Gene synonyms (human) | IPF1, STF1 |
Gene (mouse) | Pdx1 |
Gene synonyms (mouse) | Ipf1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | B |
Motif length | 10 |
Consensus | TGATWRATKR |
GC content | 30.47% |
Information content (bits; total / per base) | 11.197 / 1.12 |
Data sources | ChIP-Seq |
Aligned words | 971 |
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 | 6 (39) | 0.924 | 0.958 | 0.872 | 0.924 | 0.905 | 0.943 | 3.569 | 4.101 | 478.495 | 639.921 |
Mouse | 4 (26) | 0.805 | 0.933 | 0.677 | 0.901 | 0.733 | 0.905 | 2.223 | 3.874 | 44.62 | 384.585 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 4 experiments | median | 0.732 | 0.665 | 0.695 | 0.638 | 0.649 | 0.609 |
best | 0.778 | 0.704 | 0.74 | 0.674 | 0.7 | 0.646 | |
Methyl HT-SELEX, 1 experiments | median | 0.778 | 0.704 | 0.74 | 0.674 | 0.7 | 0.646 |
best | 0.778 | 0.704 | 0.74 | 0.674 | 0.7 | 0.646 | |
Non-Methyl HT-SELEX, 3 experiments | median | 0.709 | 0.646 | 0.664 | 0.615 | 0.61 | 0.584 |
best | 0.755 | 0.684 | 0.726 | 0.66 | 0.687 | 0.634 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 2 | 0.616 | 0.119 | 0.645 | 0.431 |
TF superclass | Helix-turn-helix domains {3} (TFClass) |
TF class | Homeo domain factors {3.1} (TFClass) |
TF family | HOX-related {3.1.1} (TFClass) |
TF subfamily | PDX {3.1.1.15} (TFClass) |
TFClass ID | TFClass: 3.1.1.15.1 |
HGNC | HGNC:6107 |
MGI | MGI:102851 |
EntrezGene (human) | GeneID:3651 (SSTAR profile) |
EntrezGene (mouse) | GeneID:18609 (SSTAR profile) |
UniProt ID (human) | PDX1_HUMAN |
UniProt ID (mouse) | PDX1_MOUSE |
UniProt AC (human) | P52945 (TFClass) |
UniProt AC (mouse) | P52946 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 6 human, 4 mouse |
HT-SELEX | 3 |
Methyl-HT-SELEX | 1 |
PCM | PDX1.H12CORE.0.P.B.pcm |
PWM | PDX1.H12CORE.0.P.B.pwm |
PFM | PDX1.H12CORE.0.P.B.pfm |
Alignment | PDX1.H12CORE.0.P.B.words.tsv |
Threshold to P-value map | PDX1.H12CORE.0.P.B.thr |
Motif in other formats | |
JASPAR format | PDX1.H12CORE.0.P.B_jaspar_format.txt |
MEME format | PDX1.H12CORE.0.P.B_meme_format.meme |
Transfac format | PDX1.H12CORE.0.P.B_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 172.0 | 2.0 | 23.0 | 774.0 |
02 | 39.0 | 7.0 | 913.0 | 12.0 |
03 | 921.0 | 22.0 | 8.0 | 20.0 |
04 | 18.0 | 96.0 | 35.0 | 822.0 |
05 | 183.0 | 7.0 | 57.0 | 724.0 |
06 | 455.0 | 13.0 | 487.0 | 16.0 |
07 | 919.0 | 14.0 | 24.0 | 14.0 |
08 | 35.0 | 35.0 | 70.0 | 831.0 |
09 | 62.0 | 41.0 | 596.0 | 272.0 |
10 | 375.0 | 38.0 | 471.0 | 87.0 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.177 | 0.002 | 0.024 | 0.797 |
02 | 0.04 | 0.007 | 0.94 | 0.012 |
03 | 0.949 | 0.023 | 0.008 | 0.021 |
04 | 0.019 | 0.099 | 0.036 | 0.847 |
05 | 0.188 | 0.007 | 0.059 | 0.746 |
06 | 0.469 | 0.013 | 0.502 | 0.016 |
07 | 0.946 | 0.014 | 0.025 | 0.014 |
08 | 0.036 | 0.036 | 0.072 | 0.856 |
09 | 0.064 | 0.042 | 0.614 | 0.28 |
10 | 0.386 | 0.039 | 0.485 | 0.09 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.342 | -4.185 | -2.291 | 1.155 |
02 | -1.792 | -3.334 | 1.32 | -2.88 |
03 | 1.328 | -2.333 | -3.225 | -2.421 |
04 | -2.517 | -0.917 | -1.896 | 1.215 |
05 | -0.28 | -3.334 | -1.426 | 1.088 |
06 | 0.625 | -2.81 | 0.693 | -2.624 |
07 | 1.326 | -2.744 | -2.252 | -2.744 |
08 | -1.896 | -1.896 | -1.226 | 1.226 |
09 | -1.345 | -1.744 | 0.894 | 0.113 |
10 | 0.432 | -1.817 | 0.659 | -1.014 |
P-value | Threshold |
---|---|
0.001 | 4.41324 |
0.0005 | 5.323135 |
0.0001 | 7.18506 |