CDX1.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

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

Motif length	11
Consensus	nbTTTATKRbn
GC content	29.84%
Information content (bits; total / per base)	11.289 / 1.026
Data sources	HT-SELEX
Aligned words	8489

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.973	0.959	0.938	0.916	0.844	0.829
Overall, 6 experiments	best	0.996	0.993	0.993	0.988	0.971	0.965
Methyl HT-SELEX, 2 experiments	median	0.98	0.968	0.951	0.935	0.861	0.852
Methyl HT-SELEX, 2 experiments	best	0.99	0.983	0.981	0.971	0.91	0.903
Non-Methyl HT-SELEX, 4 experiments	median	0.973	0.959	0.919	0.902	0.798	0.799
Non-Methyl HT-SELEX, 4 experiments	best	0.996	0.993	0.993	0.988	0.971	0.965

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.983	0.784	0.921	0.607
batch 2	0.861	0.757	0.837	0.588

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.1.S.B.pcm
PWM	CDX1.H12RSNP.1.S.B.pwm
PFM	CDX1.H12RSNP.1.S.B.pfm
Alignment	CDX1.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	CDX1.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	CDX1.H12RSNP.1.S.B_jaspar_format.txt
MEME format	CDX1.H12RSNP.1.S.B_meme_format.meme
Transfac format	CDX1.H12RSNP.1.S.B_transfac_format.txt
Homer format	CDX1.H12RSNP.1.S.B_homer_format_0.001.txt CDX1.H12RSNP.1.S.B_homer_format_0.0005.txt CDX1.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1966.75	1899.75	2745.75	1876.75
02	1205.25	1376.25	2440.25	3467.25
03	397.0	101.0	216.0	7775.0
04	7.0	20.0	8.0	8454.0
05	406.0	2.0	5.0	8076.0
06	8489.0	0.0	0.0	0.0
07	0.0	27.0	1.0	8461.0
08	128.0	109.0	3404.0	4848.0
09	3554.0	116.0	4749.0	70.0
10	580.0	4388.0	1530.0	1991.0
11	1421.5	2425.5	2301.5	2340.5

PFM

	A	C	G	T
01	0.232	0.224	0.323	0.221
02	0.142	0.162	0.287	0.408
03	0.047	0.012	0.025	0.916
04	0.001	0.002	0.001	0.996
05	0.048	0.0	0.001	0.951
06	1.0	0.0	0.0	0.0
07	0.0	0.003	0.0	0.997
08	0.015	0.013	0.401	0.571
09	0.419	0.014	0.559	0.008
10	0.068	0.517	0.18	0.235
11	0.167	0.286	0.271	0.276

PWM

	A	C	G	T
01	-0.076	-0.111	0.257	-0.123
02	-0.565	-0.433	0.139	0.49
03	-1.672	-3.024	-2.276	1.298
04	-5.435	-4.558	-5.333	1.381
05	-1.649	-6.212	-5.679	1.336
06	1.385	-6.845	-6.845	-6.845
07	-6.845	-4.285	-6.479	1.382
08	-2.792	-2.949	0.472	0.825
09	0.515	-2.888	0.805	-3.381
10	-1.294	0.726	-0.327	-0.064
11	-0.4	0.133	0.081	0.098

Standard thresholds

P-value	Threshold
0.001	4.183855
0.0005	5.199405
0.0001	7.95583