CDX2.H12INVIVO.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX2.H12INVIVO.1.M.C
Gene (human)	CDX2 (GeneCards)
Gene synonyms (human)	CDX3
Gene (mouse)	Cdx2
Gene synonyms (mouse)	Cdx-2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	10
Consensus	nWTTACGRbn
GC content	38.23%
Information content (bits; total / per base)	11.214 / 1.121
Data sources	Methyl-HT-SELEX
Aligned words	1263

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)	0.736	0.877	0.577	0.79	0.692	0.85	1.762	2.999	48.319	121.921
Mouse	21 (117)	0.774	0.877	0.638	0.767	0.709	0.83	1.934	2.468	68.444	160.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.712	0.667	0.662	0.625	0.61	0.59
Overall, 4 experiments	best	0.838	0.785	0.773	0.723	0.705	0.669
Methyl HT-SELEX, 1 experiments	median	0.838	0.785	0.773	0.723	0.705	0.669
Methyl HT-SELEX, 1 experiments	best	0.838	0.785	0.773	0.723	0.705	0.669
Non-Methyl HT-SELEX, 3 experiments	median	0.641	0.604	0.596	0.572	0.553	0.547
Non-Methyl HT-SELEX, 3 experiments	best	0.784	0.73	0.728	0.678	0.666	0.633

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.084	1.197	0.126	0.073

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.1.M.C.pcm
PWM	CDX2.H12INVIVO.1.M.C.pwm
PFM	CDX2.H12INVIVO.1.M.C.pfm
Alignment	CDX2.H12INVIVO.1.M.C.words.tsv
Threshold to P-value map	CDX2.H12INVIVO.1.M.C.thr
Motif in other formats
JASPAR format	CDX2.H12INVIVO.1.M.C_jaspar_format.txt
MEME format	CDX2.H12INVIVO.1.M.C_meme_format.meme
Transfac format	CDX2.H12INVIVO.1.M.C_transfac_format.txt
Homer format	CDX2.H12INVIVO.1.M.C_homer_format_0.001.txt CDX2.H12INVIVO.1.M.C_homer_format_0.0005.txt CDX2.H12INVIVO.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	307.75	326.75	427.75	200.75
02	223.0	37.0	125.0	878.0
03	0.0	0.0	0.0	1263.0
04	18.0	0.0	0.0	1245.0
05	1263.0	0.0	0.0	0.0
06	0.0	1077.0	0.0	186.0
07	0.0	0.0	1252.0	11.0
08	1012.0	85.0	89.0	77.0
09	79.75	433.75	232.75	516.75
10	291.0	375.0	367.0	230.0

PFM

	A	C	G	T
01	0.244	0.259	0.339	0.159
02	0.177	0.029	0.099	0.695
03	0.0	0.0	0.0	1.0
04	0.014	0.0	0.0	0.986
05	1.0	0.0	0.0	0.0
06	0.0	0.853	0.0	0.147
07	0.0	0.0	0.991	0.009
08	0.801	0.067	0.07	0.061
09	0.063	0.343	0.184	0.409
10	0.23	0.297	0.291	0.182

PWM

	A	C	G	T
01	-0.026	0.034	0.302	-0.45
02	-0.345	-2.103	-0.918	1.019
03	-5.181	-5.181	-5.181	1.382
04	-2.776	-5.181	-5.181	1.368
05	1.382	-5.181	-5.181	-5.181
06	-5.181	1.223	-5.181	-0.525
07	-5.181	-5.181	1.373	-3.212
08	1.161	-1.297	-1.252	-1.394
09	-1.36	0.316	-0.303	0.49
10	-0.081	0.171	0.15	-0.315

Standard thresholds

P-value	Threshold
0.001	4.36958
0.0005	5.53726
0.0001	7.59413