Motif | VSX2.H12CORE.0.PSM.A |
Gene (human) | VSX2 (GeneCards) |
Gene synonyms (human) | CHX10, HOX10 |
Gene (mouse) | Vsx2 |
Gene synonyms (mouse) | Chx10 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | A |
Motif | VSX2.H12CORE.0.PSM.A |
Gene (human) | VSX2 (GeneCards) |
Gene synonyms (human) | CHX10, HOX10 |
Gene (mouse) | Vsx2 |
Gene synonyms (mouse) | Chx10 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | A |
Motif length | 12 |
Consensus | vbTAATTAGChn |
GC content | 37.24% |
Information content (bits; total / per base) | 15.443 / 1.287 |
Data sources | ChIP-Seq + HT-SELEX + Methyl-HT-SELEX |
Aligned words | 9856 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|
Mouse | 1 (7) | 0.989 | 0.993 | 0.982 | 0.99 | 0.984 | 0.988 | 5.837 | 5.926 | 399.569 | 446.523 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 6 experiments | median | 0.998 | 0.997 | 0.995 | 0.993 | 0.979 | 0.973 |
best | 0.999 | 0.998 | 0.999 | 0.998 | 0.997 | 0.995 | |
Methyl HT-SELEX, 2 experiments | median | 0.992 | 0.986 | 0.988 | 0.98 | 0.97 | 0.96 |
best | 0.999 | 0.998 | 0.999 | 0.998 | 0.997 | 0.995 | |
Non-Methyl HT-SELEX, 4 experiments | median | 0.998 | 0.997 | 0.995 | 0.993 | 0.979 | 0.973 |
best | 0.998 | 0.997 | 0.996 | 0.994 | 0.992 | 0.988 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 1 | 0.959 | 0.383 | 0.95 | 0.642 |
batch 2 | 0.863 | 0.686 | 0.879 | 0.673 |
TF superclass | Helix-turn-helix domains {3} (TFClass) |
TF class | Homeo domain factors {3.1} (TFClass) |
TF family | Paired-related HD {3.1.3} (TFClass) |
TF subfamily | VSX {3.1.3.28} (TFClass) |
TFClass ID | TFClass: 3.1.3.28.2 |
HGNC | HGNC:1975 |
MGI | MGI:88401 |
EntrezGene (human) | GeneID:338917 (SSTAR profile) |
EntrezGene (mouse) | GeneID:12677 (SSTAR profile) |
UniProt ID (human) | VSX2_HUMAN |
UniProt ID (mouse) | VSX2_MOUSE |
UniProt AC (human) | P58304 (TFClass) |
UniProt AC (mouse) | Q61412 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 0 human, 1 mouse |
HT-SELEX | 4 |
Methyl-HT-SELEX | 2 |
PCM | VSX2.H12CORE.0.PSM.A.pcm |
PWM | VSX2.H12CORE.0.PSM.A.pwm |
PFM | VSX2.H12CORE.0.PSM.A.pfm |
Alignment | VSX2.H12CORE.0.PSM.A.words.tsv |
Threshold to P-value map | VSX2.H12CORE.0.PSM.A.thr |
Motif in other formats | |
JASPAR format | VSX2.H12CORE.0.PSM.A_jaspar_format.txt |
MEME format | VSX2.H12CORE.0.PSM.A_meme_format.meme |
Transfac format | VSX2.H12CORE.0.PSM.A_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 1963.0 | 3249.0 | 3403.0 | 1241.0 |
02 | 827.5 | 5349.5 | 2153.5 | 1525.5 |
03 | 129.0 | 512.0 | 30.0 | 9185.0 |
04 | 9781.0 | 5.0 | 69.0 | 1.0 |
05 | 9856.0 | 0.0 | 0.0 | 0.0 |
06 | 0.0 | 0.0 | 0.0 | 9856.0 |
07 | 0.0 | 0.0 | 0.0 | 9856.0 |
08 | 9746.0 | 0.0 | 110.0 | 0.0 |
09 | 78.0 | 276.0 | 9500.0 | 2.0 |
10 | 23.0 | 9089.0 | 530.0 | 214.0 |
11 | 1012.75 | 4554.75 | 894.75 | 3393.75 |
12 | 2994.25 | 2439.25 | 1879.25 | 2543.25 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.199 | 0.33 | 0.345 | 0.126 |
02 | 0.084 | 0.543 | 0.218 | 0.155 |
03 | 0.013 | 0.052 | 0.003 | 0.932 |
04 | 0.992 | 0.001 | 0.007 | 0.0 |
05 | 1.0 | 0.0 | 0.0 | 0.0 |
06 | 0.0 | 0.0 | 0.0 | 1.0 |
07 | 0.0 | 0.0 | 0.0 | 1.0 |
08 | 0.989 | 0.0 | 0.011 | 0.0 |
09 | 0.008 | 0.028 | 0.964 | 0.0 |
10 | 0.002 | 0.922 | 0.054 | 0.022 |
11 | 0.103 | 0.462 | 0.091 | 0.344 |
12 | 0.304 | 0.247 | 0.191 | 0.258 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.227 | 0.276 | 0.323 | -0.685 |
02 | -1.089 | 0.775 | -0.135 | -0.479 |
03 | -2.933 | -1.568 | -4.335 | 1.315 |
04 | 1.378 | -5.823 | -3.544 | -6.617 |
05 | 1.386 | -6.978 | -6.978 | -6.978 |
06 | -6.978 | -6.978 | -6.978 | 1.386 |
07 | -6.978 | -6.978 | -6.978 | 1.386 |
08 | 1.374 | -6.978 | -3.089 | -6.978 |
09 | -3.425 | -2.182 | 1.349 | -6.352 |
10 | -4.58 | 1.305 | -1.533 | -2.434 |
11 | -0.888 | 0.614 | -1.011 | 0.32 |
12 | 0.195 | -0.01 | -0.271 | 0.032 |
P-value | Threshold |
---|---|
0.001 | 0.29607 |
0.0005 | 2.18292 |
0.0001 | 5.89491 |