MotifPDX1.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 subtype1
Quality
A
Motif length13
ConsensusnvvYTAATKRbnn
GC content38.84%
Information content (bits; total / per base)11.138 / 0.857
Data sourcesChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words8990

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 superclassHelix-turn-helix domains {3} (TFClass)
TF classHomeo domain factors {3.1} (TFClass)
TF familyHOX-related {3.1.1} (TFClass)
TF subfamilyPDX {3.1.1.15} (TFClass)
TFClass IDTFClass: 3.1.1.15.1
HGNCHGNC:6107
MGIMGI: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
ACGT
012223.02189.02419.02159.0
021745.753677.752125.751440.75
032467.02402.03661.0460.0
0494.04747.0773.03376.0
050.00.00.08990.0
068990.00.00.00.0
078990.00.00.00.0
080.02.00.08988.0
091.0175.04108.04706.0
106567.092.02152.0179.0
11632.04211.02667.01480.0
121555.52897.52719.51817.5
132355.252424.251950.252260.25
PFM
ACGT
010.2470.2430.2690.24
020.1940.4090.2360.16
030.2740.2670.4070.051
040.010.5280.0860.376
050.00.00.01.0
061.00.00.00.0
071.00.00.00.0
080.00.00.01.0
090.00.0190.4570.523
100.730.010.2390.02
110.070.4680.2970.165
120.1730.3220.3030.202
130.2620.270.2170.251
PWM
ACGT
01-0.011-0.0260.073-0.04
02-0.2520.492-0.056-0.444
030.0930.0660.488-1.582
04-3.1510.747-1.0650.407
05-6.896-6.896-6.8961.386
061.386-6.896-6.896-6.896
071.386-6.896-6.896-6.896
08-6.896-6.266-6.8961.385
09-6.532-2.5410.6030.738
101.072-3.172-0.043-2.519
11-1.2660.6270.171-0.417
12-0.3680.2540.19-0.212
130.0470.076-0.1420.006
Standard thresholds
P-value Threshold
0.001 3.99901
0.0005 5.61196
0.0001 7.88571