Motif | CDX1.H12INVIVO.1.S.D |
Gene (human) | CDX1 (GeneCards) |
Gene synonyms (human) | |
Gene (mouse) | Cdx1 |
Gene synonyms (mouse) | Cdx-1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 1 |
Quality | D |
Motif | CDX1.H12INVIVO.1.S.D |
Gene (human) | CDX1 (GeneCards) |
Gene synonyms (human) | |
Gene (mouse) | Cdx1 |
Gene synonyms (mouse) | Cdx-1 |
LOGO | |
LOGO (reverse complement) | |
Motif subtype | 1 |
Quality | D |
Motif length | 13 |
Consensus | nnTTTATKGSnnn |
GC content | 36.95% |
Information content (bits; total / per base) | 11.462 / 0.882 |
Data sources | HT-SELEX |
Aligned words | 7806 |
HT-SELEX benchmarking | auROC10 | auPRC10 | auROC25 | auPRC25 | auROC50 | auPRC50 | |
---|---|---|---|---|---|---|---|
Overall, 6 experiments | median | 0.978 | 0.964 | 0.946 | 0.927 | 0.875 | 0.855 |
best | 0.996 | 0.993 | 0.994 | 0.99 | 0.975 | 0.97 | |
Methyl HT-SELEX, 2 experiments | median | 0.983 | 0.973 | 0.958 | 0.943 | 0.901 | 0.883 |
best | 0.991 | 0.984 | 0.984 | 0.975 | 0.948 | 0.933 | |
Non-Methyl HT-SELEX, 4 experiments | median | 0.978 | 0.964 | 0.928 | 0.912 | 0.814 | 0.814 |
best | 0.996 | 0.993 | 0.994 | 0.99 | 0.975 | 0.97 |
rSNP benchmarking, SNP-SELEX | auROC | auPRC | Pearson r | Kendall tau |
---|---|---|---|---|
batch 1 | 0.967 | 0.758 | 0.9 | 0.624 |
batch 2 | 0.859 | 0.771 | 0.849 | 0.584 |
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: 3.1.1.9.1 |
HGNC | HGNC:1805 |
MGI | MGI:88360 |
EntrezGene (human) | GeneID:1044 (SSTAR profile) |
EntrezGene (mouse) | GeneID:12590 (SSTAR profile) |
UniProt ID (human) | CDX1_HUMAN |
UniProt ID (mouse) | CDX1_MOUSE |
UniProt AC (human) | P47902 (TFClass) |
UniProt AC (mouse) | P18111 (TFClass) |
GRECO-DB-TF | yes |
ChIP-Seq | 0 human, 0 mouse |
HT-SELEX | 4 |
Methyl-HT-SELEX | 2 |
PCM | CDX1.H12INVIVO.1.S.D.pcm |
PWM | CDX1.H12INVIVO.1.S.D.pwm |
PFM | CDX1.H12INVIVO.1.S.D.pfm |
Alignment | CDX1.H12INVIVO.1.S.D.words.tsv |
Threshold to P-value map | CDX1.H12INVIVO.1.S.D.thr |
Motif in other formats | |
JASPAR format | CDX1.H12INVIVO.1.S.D_jaspar_format.txt |
MEME format | CDX1.H12INVIVO.1.S.D_meme_format.meme |
Transfac format | CDX1.H12INVIVO.1.S.D_transfac_format.txt |
Homer format |
A | C | G | T | |
---|---|---|---|---|
01 | 2033.5 | 1800.5 | 2521.5 | 1450.5 |
02 | 1529.75 | 1407.75 | 2554.75 | 2313.75 |
03 | 259.0 | 82.0 | 365.0 | 7100.0 |
04 | 4.0 | 9.0 | 0.0 | 7793.0 |
05 | 764.0 | 0.0 | 10.0 | 7032.0 |
06 | 7806.0 | 0.0 | 0.0 | 0.0 |
07 | 0.0 | 154.0 | 2.0 | 7650.0 |
08 | 61.0 | 10.0 | 3889.0 | 3846.0 |
09 | 3247.0 | 10.0 | 4547.0 | 2.0 |
10 | 314.0 | 4856.0 | 1494.0 | 1142.0 |
11 | 1313.0 | 2555.0 | 2294.0 | 1644.0 |
12 | 1174.5 | 2578.5 | 2388.5 | 1664.5 |
13 | 1463.0 | 2011.0 | 1957.0 | 2375.0 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.261 | 0.231 | 0.323 | 0.186 |
02 | 0.196 | 0.18 | 0.327 | 0.296 |
03 | 0.033 | 0.011 | 0.047 | 0.91 |
04 | 0.001 | 0.001 | 0.0 | 0.998 |
05 | 0.098 | 0.0 | 0.001 | 0.901 |
06 | 1.0 | 0.0 | 0.0 | 0.0 |
07 | 0.0 | 0.02 | 0.0 | 0.98 |
08 | 0.008 | 0.001 | 0.498 | 0.493 |
09 | 0.416 | 0.001 | 0.583 | 0.0 |
10 | 0.04 | 0.622 | 0.191 | 0.146 |
11 | 0.168 | 0.327 | 0.294 | 0.211 |
12 | 0.15 | 0.33 | 0.306 | 0.213 |
13 | 0.187 | 0.258 | 0.251 | 0.304 |
A | C | G | T | |
---|---|---|---|---|
01 | 0.041 | -0.08 | 0.256 | -0.296 |
02 | -0.243 | -0.326 | 0.269 | 0.17 |
03 | -2.012 | -3.144 | -1.671 | 1.291 |
04 | -5.746 | -5.158 | -6.771 | 1.384 |
05 | -0.936 | -6.771 | -5.073 | 1.281 |
06 | 1.385 | -6.771 | -6.771 | -6.771 |
07 | -6.771 | -2.526 | -6.133 | 1.365 |
08 | -3.431 | -5.073 | 0.689 | 0.678 |
09 | 0.509 | -5.073 | 0.845 | -6.133 |
10 | -1.821 | 0.911 | -0.267 | -0.535 |
11 | -0.396 | 0.269 | 0.162 | -0.171 |
12 | -0.507 | 0.278 | 0.202 | -0.159 |
13 | -0.288 | 0.03 | 0.003 | 0.196 |
P-value | Threshold |
---|---|
0.001 | 3.93406 |
0.0005 | 5.27386 |
0.0001 | 7.7955 |