CDX4.H12RSNP.0.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX4.H12RSNP.0.S.C
Gene (human)	CDX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx4
Gene synonyms (mouse)	Cdx-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	12
Consensus	nvKTTTATGRCh
GC content	34.63%
Information content (bits; total / per base)	14.557 / 1.213
Data sources	HT-SELEX
Aligned words	8403

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.969	0.959	0.907	0.899	0.82	0.832
Overall, 2 experiments	best	0.998	0.997	0.996	0.994	0.984	0.98
Methyl HT-SELEX, 1 experiments	median	0.94	0.921	0.817	0.804	0.656	0.684
Methyl HT-SELEX, 1 experiments	best	0.94	0.921	0.817	0.804	0.656	0.684
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.996	0.994	0.984	0.98
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.996	0.994	0.984	0.98

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.768	0.614	0.791	0.565

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: 3.1.1.9.3
HGNC	HGNC:1808
MGI	MGI:88362
EntrezGene (human)	GeneID:1046 (SSTAR profile)
EntrezGene (mouse)	GeneID:12592 (SSTAR profile)
UniProt ID (human)	CDX4_HUMAN
UniProt ID (mouse)	CDX4_MOUSE
UniProt AC (human)	O14627 (TFClass)
UniProt AC (mouse)	Q07424 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	CDX4.H12RSNP.0.S.C.pcm
PWM	CDX4.H12RSNP.0.S.C.pwm
PFM	CDX4.H12RSNP.0.S.C.pfm
Alignment	CDX4.H12RSNP.0.S.C.words.tsv
Threshold to P-value map	CDX4.H12RSNP.0.S.C.thr
Motif in other formats
JASPAR format	CDX4.H12RSNP.0.S.C_jaspar_format.txt
MEME format	CDX4.H12RSNP.0.S.C_meme_format.meme
Transfac format	CDX4.H12RSNP.0.S.C_transfac_format.txt
Homer format	CDX4.H12RSNP.0.S.C_homer_format_0.001.txt CDX4.H12RSNP.0.S.C_homer_format_0.0005.txt CDX4.H12RSNP.0.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2324.75	2131.75	2150.75	1795.75
02	1441.0	1565.0	4362.0	1035.0
03	453.0	356.0	1225.0	6369.0
04	0.0	0.0	0.0	8403.0
05	0.0	0.0	0.0	8403.0
06	0.0	0.0	0.0	8403.0
07	8403.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8403.0
09	4.0	1.0	5623.0	2775.0
10	3717.0	2.0	4676.0	8.0
11	154.5	7182.5	386.5	679.5
12	1679.5	3876.5	1378.5	1468.5

PFM

	A	C	G	T
01	0.277	0.254	0.256	0.214
02	0.171	0.186	0.519	0.123
03	0.054	0.042	0.146	0.758
04	0.0	0.0	0.0	1.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.669	0.33
10	0.442	0.0	0.556	0.001
11	0.018	0.855	0.046	0.081
12	0.2	0.461	0.164	0.175

PWM

	A	C	G	T
01	0.101	0.015	0.023	-0.157
02	-0.376	-0.294	0.73	-0.707
03	-1.53	-1.77	-0.539	1.108
04	-6.836	-6.836	-6.836	1.385
05	-6.836	-6.836	-6.836	1.385
06	-6.836	-6.836	-6.836	1.385
07	1.385	-6.836	-6.836	-6.836
08	-6.836	-6.836	-6.836	1.385
09	-5.817	-6.47	0.984	0.278
10	0.57	-6.202	0.8	-5.323
11	-2.596	1.229	-1.688	-1.126
12	-0.224	0.612	-0.421	-0.358

Standard thresholds

P-value	Threshold
0.001	0.13148
0.0005	1.63513
0.0001	6.63286