Motif | CDX2.H12INVIVO.0.PS.A |
Gene (human) | CDX2 (GeneCards) |
Gene synonyms (human) | CDX3 |
Gene (mouse) | Cdx2 |
Gene synonyms (mouse) | Cdx-2 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | A |
Motif | CDX2.H12INVIVO.0.PS.A |
Gene (human) | CDX2 (GeneCards) |
Gene synonyms (human) | CDX3 |
Gene (mouse) | Cdx2 |
Gene synonyms (mouse) | Cdx-2 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 0 |
Quality | A |
Motif length | 13 |
Consensus | nbTTTATKRChbb |
GC content | 33.58% |
Information content (bits; total / per base) | 12.727 / 0.979 |
Data sources | ChIP-Seq + HT-SELEX |
Aligned words | 1000 |
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 | 10 (61) | 0.828 | 0.976 | 0.696 | 0.945 | 0.825 | 0.979 | 2.778 | 5.069 | 102.18 | 288.201 |
Mouse | 21 (117) | 0.878 | 0.978 | 0.83 | 0.965 | 0.878 | 0.975 | 3.428 | 5.276 | 150.886 | 401.77 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 4 experiments | median | 0.805 | 0.76 | 0.706 | 0.679 | 0.631 | 0.622 |
best | 0.856 | 0.798 | 0.782 | 0.734 | 0.695 | 0.669 | |
Methyl HT-SELEX, 1 experiments | median | 0.831 | 0.764 | 0.768 | 0.712 | 0.695 | 0.659 |
best | 0.831 | 0.764 | 0.768 | 0.712 | 0.695 | 0.659 | |
Non-Methyl HT-SELEX, 3 experiments | median | 0.778 | 0.756 | 0.643 | 0.646 | 0.567 | 0.585 |
best | 0.856 | 0.798 | 0.782 | 0.734 | 0.695 | 0.669 |
rSNP benchmarking, ADASTRA | odds-ratio | -log-Fisher's P | Pearson r | Kendall tau |
---|---|---|---|---|
# | 7.658 | 5.658 | 0.314 | 0.208 |
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 | CDX {3.1.1.9} (TFClass) |
TFClass ID | TFClass: 3.1.1.9.2 |
HGNC | HGNC:1806 |
MGI | MGI:88361 |
EntrezGene (human) | GeneID:1045 (SSTAR profile) |
EntrezGene (mouse) | GeneID:12591 (SSTAR profile) |
UniProt ID (human) | CDX2_HUMAN |
UniProt ID (mouse) | CDX2_MOUSE |
UniProt AC (human) | Q99626 (TFClass) |
UniProt AC (mouse) | P43241 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 10 human, 21 mouse |
HT-SELEX | 3 |
Methyl-HT-SELEX | 1 |
PCM | CDX2.H12INVIVO.0.PS.A.pcm |
PWM | CDX2.H12INVIVO.0.PS.A.pwm |
PFM | CDX2.H12INVIVO.0.PS.A.pfm |
Alignment | CDX2.H12INVIVO.0.PS.A.words.tsv |
Threshold to P-value map | CDX2.H12INVIVO.0.PS.A.thr |
Motif in other formats | |
JASPAR format | CDX2.H12INVIVO.0.PS.A_jaspar_format.txt |
MEME format | CDX2.H12INVIVO.0.PS.A_meme_format.meme |
Transfac format | CDX2.H12INVIVO.0.PS.A_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 191.0 | 173.0 | 382.0 | 254.0 |
02 | 117.0 | 145.0 | 173.0 | 565.0 |
03 | 8.0 | 6.0 | 10.0 | 976.0 |
04 | 11.0 | 5.0 | 1.0 | 983.0 |
05 | 35.0 | 19.0 | 17.0 | 929.0 |
06 | 998.0 | 1.0 | 1.0 | 0.0 |
07 | 3.0 | 46.0 | 0.0 | 951.0 |
08 | 41.0 | 4.0 | 524.0 | 431.0 |
09 | 430.0 | 3.0 | 562.0 | 5.0 |
10 | 18.0 | 809.0 | 58.0 | 115.0 |
11 | 158.0 | 472.0 | 45.0 | 325.0 |
12 | 98.0 | 335.0 | 180.0 | 387.0 |
13 | 134.0 | 247.0 | 148.0 | 471.0 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.191 | 0.173 | 0.382 | 0.254 |
02 | 0.117 | 0.145 | 0.173 | 0.565 |
03 | 0.008 | 0.006 | 0.01 | 0.976 |
04 | 0.011 | 0.005 | 0.001 | 0.983 |
05 | 0.035 | 0.019 | 0.017 | 0.929 |
06 | 0.998 | 0.001 | 0.001 | 0.0 |
07 | 0.003 | 0.046 | 0.0 | 0.951 |
08 | 0.041 | 0.004 | 0.524 | 0.431 |
09 | 0.43 | 0.003 | 0.562 | 0.005 |
10 | 0.018 | 0.809 | 0.058 | 0.115 |
11 | 0.158 | 0.472 | 0.045 | 0.325 |
12 | 0.098 | 0.335 | 0.18 | 0.387 |
13 | 0.134 | 0.247 | 0.148 | 0.471 |
A | C | G | T | |
---|---|---|---|---|
01 | -0.267 | -0.365 | 0.422 | 0.016 |
02 | -0.752 | -0.54 | -0.365 | 0.812 |
03 | -3.253 | -3.484 | -3.066 | 1.357 |
04 | -2.985 | -3.622 | -4.525 | 1.364 |
05 | -1.925 | -2.497 | -2.598 | 1.308 |
06 | 1.379 | -4.525 | -4.525 | -4.982 |
07 | -3.975 | -1.663 | -4.982 | 1.331 |
08 | -1.774 | -3.783 | 0.736 | 0.542 |
09 | 0.539 | -3.975 | 0.806 | -3.622 |
10 | -2.546 | 1.17 | -1.439 | -0.769 |
11 | -0.455 | 0.632 | -1.684 | 0.261 |
12 | -0.926 | 0.291 | -0.326 | 0.435 |
13 | -0.618 | -0.012 | -0.52 | 0.63 |
P-value | Threshold |
---|---|
0.001 | 3.69616 |
0.0005 | 4.84236 |
0.0001 | 7.15956 |