CDX2.H13INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX2.H13INVIVO.0.PS.A
Gene (human)	CDX2 (GeneCards)
Gene synonyms (human)	CDX3
Gene (mouse)	Cdx2
Gene synonyms (mouse)	Cdx-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nbTTTATKRChbb
GC content	33.58%
Information content (bits; total / per base)	12.727 / 0.979
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000
Previous names	CDX2.H12INVIVO.0.PS.A

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)	0.828	0.976	0.696	0.945	0.825	0.979	2.778	5.069	102.18	288.201
Mouse	21 (117)	0.878	0.978	0.83	0.965	0.878	0.975	3.428	5.276	150.886	401.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.805	0.76	0.706	0.679	0.631	0.622
Overall, 4 experiments	best	0.856	0.798	0.782	0.734	0.695	0.669
Methyl HT-SELEX, 1 experiments	median	0.831	0.764	0.768	0.712	0.695	0.659
Methyl HT-SELEX, 1 experiments	best	0.831	0.764	0.768	0.712	0.695	0.659
Non-Methyl HT-SELEX, 3 experiments	median	0.778	0.756	0.643	0.646	0.567	0.585
Non-Methyl HT-SELEX, 3 experiments	best	0.856	0.798	0.782	0.734	0.695	0.669

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.658	5.658	0.314	0.208

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	CDX2.H13INVIVO.0.PS.A.pcm
PWM	CDX2.H13INVIVO.0.PS.A.pwm
PFM	CDX2.H13INVIVO.0.PS.A.pfm
Threshold to P-value map	CDX2.H13INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	CDX2.H13INVIVO.0.PS.A_jaspar_format.txt
MEME format	CDX2.H13INVIVO.0.PS.A_meme_format.meme
Transfac format	CDX2.H13INVIVO.0.PS.A_transfac_format.txt
Homer format	CDX2.H13INVIVO.0.PS.A_homer_format_0.001.txt CDX2.H13INVIVO.0.PS.A_homer_format_0.0005.txt CDX2.H13INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	191.0	173.0	382.0	254.0
02	117.0	145.0	173.0	565.0
03	8.0	6.0	10.0	976.0
04	11.0	5.0	1.0	983.0
05	35.0	19.0	17.0	929.0
06	998.0	1.0	1.0	0.0
07	3.0	46.0	0.0	951.0
08	41.0	4.0	524.0	431.0
09	430.0	3.0	562.0	5.0
10	18.0	809.0	58.0	115.0
11	158.0	472.0	45.0	325.0
12	98.0	335.0	180.0	387.0
13	134.0	247.0	148.0	471.0

PFM

	A	C	G	T
01	0.191	0.173	0.382	0.254
02	0.117	0.145	0.173	0.565
03	0.008	0.006	0.01	0.976
04	0.011	0.005	0.001	0.983
05	0.035	0.019	0.017	0.929
06	0.998	0.001	0.001	0.0
07	0.003	0.046	0.0	0.951
08	0.041	0.004	0.524	0.431
09	0.43	0.003	0.562	0.005
10	0.018	0.809	0.058	0.115
11	0.158	0.472	0.045	0.325
12	0.098	0.335	0.18	0.387
13	0.134	0.247	0.148	0.471

PWM

	A	C	G	T
01	-0.267	-0.365	0.422	0.016
02	-0.752	-0.54	-0.365	0.812
03	-3.253	-3.484	-3.066	1.357
04	-2.985	-3.622	-4.525	1.364
05	-1.925	-2.497	-2.598	1.308
06	1.379	-4.525	-4.525	-4.982
07	-3.975	-1.663	-4.982	1.331
08	-1.774	-3.783	0.736	0.542
09	0.539	-3.975	0.806	-3.622
10	-2.546	1.17	-1.439	-0.769
11	-0.455	0.632	-1.684	0.261
12	-0.926	0.291	-0.326	0.435
13	-0.618	-0.012	-0.52	0.63

Standard thresholds

P-value	Threshold
0.001	3.69616
0.0005	4.84236
0.0001	7.15956