CDX1.H12RSNP.0.M.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX1.H12RSNP.0.M.B
Gene (human)	CDX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx1
Gene synonyms (mouse)	Cdx-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	nnTTTACGAYn
GC content	36.52%
Information content (bits; total / per base)	10.855 / 0.987
Data sources	Methyl-HT-SELEX
Aligned words	9752

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.974	0.956	0.948	0.925	0.867	0.848
Overall, 6 experiments	best	0.998	0.996	0.996	0.994	0.989	0.985
Methyl HT-SELEX, 2 experiments	median	0.992	0.988	0.979	0.971	0.933	0.925
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.996	0.994	0.989	0.985
Non-Methyl HT-SELEX, 4 experiments	median	0.948	0.918	0.898	0.866	0.785	0.775
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.98	0.984	0.973	0.963	0.949

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.884	0.507	0.839	0.542
batch 2	0.823	0.666	0.759	0.507

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.H12RSNP.0.M.B.pcm
PWM	CDX1.H12RSNP.0.M.B.pwm
PFM	CDX1.H12RSNP.0.M.B.pfm
Alignment	CDX1.H12RSNP.0.M.B.words.tsv
Threshold to P-value map	CDX1.H12RSNP.0.M.B.thr
Motif in other formats
JASPAR format	CDX1.H12RSNP.0.M.B_jaspar_format.txt
MEME format	CDX1.H12RSNP.0.M.B_meme_format.meme
Transfac format	CDX1.H12RSNP.0.M.B_transfac_format.txt
Homer format	CDX1.H12RSNP.0.M.B_homer_format_0.001.txt CDX1.H12RSNP.0.M.B_homer_format_0.0005.txt CDX1.H12RSNP.0.M.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2651.5	2280.5	2789.5	2030.5
02	2081.25	1865.25	2696.25	3109.25
03	903.0	144.0	276.0	8429.0
04	51.0	54.0	31.0	9616.0
05	355.0	23.0	90.0	9284.0
06	9738.0	3.0	11.0	0.0
07	0.0	5588.0	1.0	4163.0
08	126.0	12.0	8272.0	1342.0
09	7504.0	120.0	1929.0	199.0
10	235.25	6218.25	1103.25	2195.25
11	2160.75	2672.75	2998.75	1919.75

PFM

	A	C	G	T
01	0.272	0.234	0.286	0.208
02	0.213	0.191	0.276	0.319
03	0.093	0.015	0.028	0.864
04	0.005	0.006	0.003	0.986
05	0.036	0.002	0.009	0.952
06	0.999	0.0	0.001	0.0
07	0.0	0.573	0.0	0.427
08	0.013	0.001	0.848	0.138
09	0.769	0.012	0.198	0.02
10	0.024	0.638	0.113	0.225
11	0.222	0.274	0.308	0.197

PWM

	A	C	G	T
01	0.084	-0.067	0.135	-0.183
02	-0.158	-0.267	0.101	0.243
03	-0.992	-2.814	-2.171	1.24
04	-3.824	-3.769	-4.294	1.372
05	-1.921	-4.569	-3.275	1.336
06	1.384	-6.133	-5.212	-6.969
07	-6.969	0.829	-6.607	0.535
08	-2.946	-5.14	1.221	-0.596
09	1.124	-2.993	-0.234	-2.495
10	-2.33	0.936	-0.792	-0.105
11	-0.121	0.092	0.207	-0.239

Standard thresholds

P-value	Threshold
0.001	4.38103
0.0005	5.524335
0.0001	7.67941