Motif | PDX1.H12CORE.1.PSM.A |
Gene (human) | PDX1 (GeneCards) |
Gene synonyms (human) | IPF1, STF1 |
Gene (mouse) | Pdx1 |
Gene synonyms (mouse) | Ipf1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 1 |
Quality | A |
Motif | PDX1.H12CORE.1.PSM.A |
Gene (human) | PDX1 (GeneCards) |
Gene synonyms (human) | IPF1, STF1 |
Gene (mouse) | Pdx1 |
Gene synonyms (mouse) | Ipf1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 1 |
Quality | A |
Motif length | 13 |
Consensus | nvvYTAATKRbnn |
GC content | 38.84% |
Information content (bits; total / per base) | 11.138 / 0.857 |
Data sources | ChIP-Seq + HT-SELEX + Methyl-HT-SELEX |
Aligned words | 8990 |
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) | 0.623 | 0.643 | 0.469 | 0.497 | 0.576 | 0.593 | 1.34 | 1.418 | 39.114 | 61.31 |
Mouse | 4 (26) | 0.646 | 0.91 | 0.473 | 0.84 | 0.532 | 0.852 | 1.197 | 2.511 | 27.665 | 125.481 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 4 experiments | median | 0.973 | 0.957 | 0.929 | 0.91 | 0.834 | 0.831 |
best | 0.984 | 0.973 | 0.974 | 0.959 | 0.957 | 0.936 | |
Methyl HT-SELEX, 1 experiments | median | 0.984 | 0.973 | 0.974 | 0.959 | 0.957 | 0.936 |
best | 0.984 | 0.973 | 0.974 | 0.959 | 0.957 | 0.936 | |
Non-Methyl HT-SELEX, 3 experiments | median | 0.967 | 0.952 | 0.891 | 0.873 | 0.724 | 0.743 |
best | 0.978 | 0.963 | 0.967 | 0.947 | 0.945 | 0.92 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 2 | 0.852 | 0.589 | 0.849 | 0.632 |
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.1.PSM.A.pcm |
PWM | PDX1.H12CORE.1.PSM.A.pwm |
PFM | PDX1.H12CORE.1.PSM.A.pfm |
Alignment | PDX1.H12CORE.1.PSM.A.words.tsv |
Threshold to P-value map | PDX1.H12CORE.1.PSM.A.thr |
Motif in other formats | |
JASPAR format | PDX1.H12CORE.1.PSM.A_jaspar_format.txt |
MEME format | PDX1.H12CORE.1.PSM.A_meme_format.meme |
Transfac format | PDX1.H12CORE.1.PSM.A_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 2223.0 | 2189.0 | 2419.0 | 2159.0 |
02 | 1745.75 | 3677.75 | 2125.75 | 1440.75 |
03 | 2467.0 | 2402.0 | 3661.0 | 460.0 |
04 | 94.0 | 4747.0 | 773.0 | 3376.0 |
05 | 0.0 | 0.0 | 0.0 | 8990.0 |
06 | 8990.0 | 0.0 | 0.0 | 0.0 |
07 | 8990.0 | 0.0 | 0.0 | 0.0 |
08 | 0.0 | 2.0 | 0.0 | 8988.0 |
09 | 1.0 | 175.0 | 4108.0 | 4706.0 |
10 | 6567.0 | 92.0 | 2152.0 | 179.0 |
11 | 632.0 | 4211.0 | 2667.0 | 1480.0 |
12 | 1555.5 | 2897.5 | 2719.5 | 1817.5 |
13 | 2355.25 | 2424.25 | 1950.25 | 2260.25 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.247 | 0.243 | 0.269 | 0.24 |
02 | 0.194 | 0.409 | 0.236 | 0.16 |
03 | 0.274 | 0.267 | 0.407 | 0.051 |
04 | 0.01 | 0.528 | 0.086 | 0.376 |
05 | 0.0 | 0.0 | 0.0 | 1.0 |
06 | 1.0 | 0.0 | 0.0 | 0.0 |
07 | 1.0 | 0.0 | 0.0 | 0.0 |
08 | 0.0 | 0.0 | 0.0 | 1.0 |
09 | 0.0 | 0.019 | 0.457 | 0.523 |
10 | 0.73 | 0.01 | 0.239 | 0.02 |
11 | 0.07 | 0.468 | 0.297 | 0.165 |
12 | 0.173 | 0.322 | 0.303 | 0.202 |
13 | 0.262 | 0.27 | 0.217 | 0.251 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.011 | -0.026 | 0.073 | -0.04 |
02 | -0.252 | 0.492 | -0.056 | -0.444 |
03 | 0.093 | 0.066 | 0.488 | -1.582 |
04 | -3.151 | 0.747 | -1.065 | 0.407 |
05 | -6.896 | -6.896 | -6.896 | 1.386 |
06 | 1.386 | -6.896 | -6.896 | -6.896 |
07 | 1.386 | -6.896 | -6.896 | -6.896 |
08 | -6.896 | -6.266 | -6.896 | 1.385 |
09 | -6.532 | -2.541 | 0.603 | 0.738 |
10 | 1.072 | -3.172 | -0.043 | -2.519 |
11 | -1.266 | 0.627 | 0.171 | -0.417 |
12 | -0.368 | 0.254 | 0.19 | -0.212 |
13 | 0.047 | 0.076 | -0.142 | 0.006 |
P-value | Threshold |
---|---|
0.001 | 3.99901 |
0.0005 | 5.61196 |
0.0001 | 7.88571 |