MotifPKNX1.H12INVIVO.3.SM.B
Gene (human)PKNOX1
(GeneCards)
Gene synonyms (human)PREP1
Gene (mouse)Pknox1
Gene synonyms (mouse)Prep1
LOGO
LOGO (reverse complement)
Motif subtype3
Quality
B
Motif length14
ConsensusnndTGACAGSKKdb
GC content52.45%
Information content (bits; total / per base)14.736 / 1.053
Data sourcesHT-SELEX + Methyl-HT-SELEX
Aligned words681

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 (35) 0.64 0.74 0.508 0.597 0.64 0.747 1.657 2.089 99.237 161.585
Mouse 5 (35) 0.63 0.691 0.487 0.547 0.653 0.708 1.75 2.032 85.119 172.42

HT-SELEX benchmarking auROC10 auPRC10 auROC25 auPRC25 auROC50 auPRC50
Overall, 6 experiments median 0.861 0.849 0.751 0.748 0.648 0.661
best 0.99 0.987 0.948 0.934 0.854 0.841
Methyl HT-SELEX, 2 experiments median 0.845 0.825 0.743 0.736 0.642 0.654
best 0.959 0.944 0.88 0.86 0.74 0.744
Non-Methyl HT-SELEX, 4 experiments median 0.87 0.861 0.783 0.783 0.686 0.698
best 0.99 0.987 0.948 0.934 0.854 0.841

rSNP benchmarking, ADASTRA odds-ratio -log-Fisher's P Pearson r Kendall tau
# 4.16 13.107 0.173 0.13
TF superclassHelix-turn-helix domains {3} (TFClass)
TF classHomeo domain factors {3.1} (TFClass)
TF familyTALE-type HD {3.1.4} (TFClass)
TF subfamilyPKNOX {3.1.4.5} (TFClass)
TFClass IDTFClass: 3.1.4.5.1
HGNCHGNC:9022
MGIMGI:1201409
EntrezGene (human)GeneID:5316
(SSTAR profile)
EntrezGene (mouse)GeneID:18771
(SSTAR profile)
UniProt ID (human)PKNX1_HUMAN
UniProt ID (mouse)PKNX1_MOUSE
UniProt AC (human)P55347
(TFClass)
UniProt AC (mouse)O70477
(TFClass)
GRECO-DB-TF
yes
ChIP-Seq 5 human, 5 mouse
HT-SELEX 4
Methyl-HT-SELEX 2
PCM
ACGT
01163.75147.75228.75140.75
02203.2583.25186.25208.25
03111.080.0251.0239.0
040.025.00.0656.0
050.00.0681.00.0
06681.00.00.00.0
070.0680.01.00.0
08681.00.00.00.0
090.018.0622.041.0
1049.0247.0374.011.0
1119.056.068.0538.0
1253.032.0542.054.0
13129.061.0111.0380.0
1464.5388.5117.5110.5
PFM
ACGT
010.240.2170.3360.207
020.2980.1220.2730.306
030.1630.1170.3690.351
040.00.0370.00.963
050.00.01.00.0
061.00.00.00.0
070.00.9990.0010.0
081.00.00.00.0
090.00.0260.9130.06
100.0720.3630.5490.016
110.0280.0820.10.79
120.0780.0470.7960.079
130.1890.090.1630.558
140.0950.570.1730.162
PWM
ACGT
01-0.039-0.140.293-0.188
020.176-0.7060.0890.2
03-0.423-0.7450.3850.336
04-4.658-1.865-4.6581.342
05-4.658-4.6581.379-4.658
061.379-4.658-4.658-4.658
07-4.6581.378-4.179-4.658
081.379-4.658-4.658-4.658
09-4.658-2.171.289-1.394
10-1.2220.3690.782-2.611
11-2.12-1.093-0.9041.144
12-1.146-1.6311.151-1.128
13-0.274-1.01-0.4230.798
14-0.9550.82-0.367-0.427
Standard thresholds
P-value Threshold
0.001 2.54731
0.0005 3.88756
0.0001 6.70766