Motif | PKNX1.H12CORE.3.SM.B |
Gene (human) | PKNOX1 (GeneCards) |
Gene synonyms (human) | PREP1 |
Gene (mouse) | Pknox1 |
Gene synonyms (mouse) | Prep1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 3 |
Quality | B |
Motif | PKNX1.H12CORE.3.SM.B |
Gene (human) | PKNOX1 (GeneCards) |
Gene synonyms (human) | PREP1 |
Gene (mouse) | Pknox1 |
Gene synonyms (mouse) | Prep1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 3 |
Quality | B |
Motif length | 14 |
Consensus | nndTGACAGSKKdb |
GC content | 52.45% |
Information content (bits; total / per base) | 14.736 / 1.053 |
Data sources | HT-SELEX + Methyl-HT-SELEX |
Aligned words | 681 |
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 superclass | Helix-turn-helix domains {3} (TFClass) |
TF class | Homeo domain factors {3.1} (TFClass) |
TF family | TALE-type HD {3.1.4} (TFClass) |
TF subfamily | PKNOX {3.1.4.5} (TFClass) |
TFClass ID | TFClass: 3.1.4.5.1 |
HGNC | HGNC:9022 |
MGI | MGI: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 | PKNX1.H12CORE.3.SM.B.pcm |
PWM | PKNX1.H12CORE.3.SM.B.pwm |
PFM | PKNX1.H12CORE.3.SM.B.pfm |
Alignment | PKNX1.H12CORE.3.SM.B.words.tsv |
Threshold to P-value map | PKNX1.H12CORE.3.SM.B.thr |
Motif in other formats | |
JASPAR format | PKNX1.H12CORE.3.SM.B_jaspar_format.txt |
MEME format | PKNX1.H12CORE.3.SM.B_meme_format.meme |
Transfac format | PKNX1.H12CORE.3.SM.B_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 163.75 | 147.75 | 228.75 | 140.75 |
02 | 203.25 | 83.25 | 186.25 | 208.25 |
03 | 111.0 | 80.0 | 251.0 | 239.0 |
04 | 0.0 | 25.0 | 0.0 | 656.0 |
05 | 0.0 | 0.0 | 681.0 | 0.0 |
06 | 681.0 | 0.0 | 0.0 | 0.0 |
07 | 0.0 | 680.0 | 1.0 | 0.0 |
08 | 681.0 | 0.0 | 0.0 | 0.0 |
09 | 0.0 | 18.0 | 622.0 | 41.0 |
10 | 49.0 | 247.0 | 374.0 | 11.0 |
11 | 19.0 | 56.0 | 68.0 | 538.0 |
12 | 53.0 | 32.0 | 542.0 | 54.0 |
13 | 129.0 | 61.0 | 111.0 | 380.0 |
14 | 64.5 | 388.5 | 117.5 | 110.5 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.24 | 0.217 | 0.336 | 0.207 |
02 | 0.298 | 0.122 | 0.273 | 0.306 |
03 | 0.163 | 0.117 | 0.369 | 0.351 |
04 | 0.0 | 0.037 | 0.0 | 0.963 |
05 | 0.0 | 0.0 | 1.0 | 0.0 |
06 | 1.0 | 0.0 | 0.0 | 0.0 |
07 | 0.0 | 0.999 | 0.001 | 0.0 |
08 | 1.0 | 0.0 | 0.0 | 0.0 |
09 | 0.0 | 0.026 | 0.913 | 0.06 |
10 | 0.072 | 0.363 | 0.549 | 0.016 |
11 | 0.028 | 0.082 | 0.1 | 0.79 |
12 | 0.078 | 0.047 | 0.796 | 0.079 |
13 | 0.189 | 0.09 | 0.163 | 0.558 |
14 | 0.095 | 0.57 | 0.173 | 0.162 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.039 | -0.14 | 0.293 | -0.188 |
02 | 0.176 | -0.706 | 0.089 | 0.2 |
03 | -0.423 | -0.745 | 0.385 | 0.336 |
04 | -4.658 | -1.865 | -4.658 | 1.342 |
05 | -4.658 | -4.658 | 1.379 | -4.658 |
06 | 1.379 | -4.658 | -4.658 | -4.658 |
07 | -4.658 | 1.378 | -4.179 | -4.658 |
08 | 1.379 | -4.658 | -4.658 | -4.658 |
09 | -4.658 | -2.17 | 1.289 | -1.394 |
10 | -1.222 | 0.369 | 0.782 | -2.611 |
11 | -2.12 | -1.093 | -0.904 | 1.144 |
12 | -1.146 | -1.631 | 1.151 | -1.128 |
13 | -0.274 | -1.01 | -0.423 | 0.798 |
14 | -0.955 | 0.82 | -0.367 | -0.427 |
P-value | Threshold |
---|---|
0.001 | 2.54731 |
0.0005 | 3.88756 |
0.0001 | 6.70766 |