CDX4.H12INVIVO.0.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX4.H12INVIVO.0.S.D
Gene (human)	CDX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx4
Gene synonyms (mouse)	Cdx-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	14
Consensus	nvKTTTATGRCvbn
GC content	38.76%
Information content (bits; total / per base)	14.702 / 1.05
Data sources	HT-SELEX
Aligned words	2227

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.97	0.961	0.911	0.904	0.826	0.836
Overall, 2 experiments	best	0.999	0.998	0.997	0.995	0.984	0.981
Methyl HT-SELEX, 1 experiments	median	0.941	0.925	0.826	0.813	0.667	0.692
Methyl HT-SELEX, 1 experiments	best	0.941	0.925	0.826	0.813	0.667	0.692
Non-Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.997	0.995	0.984	0.981
Non-Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.997	0.995	0.984	0.981

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.764	0.586	0.783	0.564

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.H12INVIVO.0.S.D.pcm
PWM	CDX4.H12INVIVO.0.S.D.pwm
PFM	CDX4.H12INVIVO.0.S.D.pfm
Alignment	CDX4.H12INVIVO.0.S.D.words.tsv
Threshold to P-value map	CDX4.H12INVIVO.0.S.D.thr
Motif in other formats
JASPAR format	CDX4.H12INVIVO.0.S.D_jaspar_format.txt
MEME format	CDX4.H12INVIVO.0.S.D_meme_format.meme
Transfac format	CDX4.H12INVIVO.0.S.D_transfac_format.txt
Homer format	CDX4.H12INVIVO.0.S.D_homer_format_0.001.txt CDX4.H12INVIVO.0.S.D_homer_format_0.0005.txt CDX4.H12INVIVO.0.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	626.0	588.0	550.0	463.0
02	418.5	437.5	1081.5	289.5
03	115.0	129.0	431.0	1552.0
04	1.0	0.0	1.0	2225.0
05	0.0	0.0	0.0	2227.0
06	0.0	0.0	0.0	2227.0
07	2227.0	0.0	0.0	0.0
08	0.0	0.0	0.0	2227.0
09	1.0	0.0	1625.0	601.0
10	1122.0	2.0	1102.0	1.0
11	24.0	1924.0	74.0	205.0
12	441.0	1034.0	388.0	364.0
13	268.25	980.25	538.25	440.25
14	317.25	725.25	473.25	711.25

PFM

	A	C	G	T
01	0.281	0.264	0.247	0.208
02	0.188	0.196	0.486	0.13
03	0.052	0.058	0.194	0.697
04	0.0	0.0	0.0	0.999
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	0.73	0.27
10	0.504	0.001	0.495	0.0
11	0.011	0.864	0.033	0.092
12	0.198	0.464	0.174	0.163
13	0.12	0.44	0.242	0.198
14	0.142	0.326	0.213	0.319

PWM

	A	C	G	T
01	0.117	0.054	-0.012	-0.184
02	-0.284	-0.24	0.662	-0.651
03	-1.564	-1.451	-0.255	1.023
04	-5.252	-5.67	-5.252	1.383
05	-5.67	-5.67	-5.67	1.384
06	-5.67	-5.67	-5.67	1.384
07	1.384	-5.67	-5.67	-5.67
08	-5.67	-5.67	-5.67	1.384
09	-5.252	-5.67	1.069	0.076
10	0.699	-4.958	0.681	-5.252
11	-3.07	1.238	-1.996	-0.993
12	-0.232	0.617	-0.36	-0.423
13	-0.726	0.564	-0.034	-0.234
14	-0.56	0.264	-0.162	0.244

Standard thresholds

P-value	Threshold
0.001	1.22261
0.0005	2.67881
0.0001	6.44491