CDX1.H12INVIVO.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

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
Overall, 6 experiments	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
Methyl HT-SELEX, 2 experiments	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
Non-Methyl HT-SELEX, 4 experiments	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	CDX1.H12INVIVO.1.S.D_homer_format_0.001.txt CDX1.H12INVIVO.1.S.D_homer_format_0.0005.txt CDX1.H12INVIVO.1.S.D_homer_format_0.0001.txt

PCM

	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

PFM

	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

PWM

	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

Standard thresholds

P-value	Threshold
0.001	3.93406
0.0005	5.27386
0.0001	7.7955