CDX4.H12INVIVO.1.M.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX4.H12INVIVO.1.M.D
Gene (human)	CDX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx4
Gene synonyms (mouse)	Cdx-4
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	13
Consensus	ndTTTACGACvbn
GC content	43.1%
Information content (bits; total / per base)	14.544 / 1.119
Data sources	Methyl-HT-SELEX
Aligned words	6856

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.985	0.979	0.924	0.917	0.831	0.837
Overall, 2 experiments	best	0.989	0.98	0.98	0.969	0.96	0.945
Methyl HT-SELEX, 1 experiments	median	0.982	0.977	0.868	0.865	0.701	0.729
Methyl HT-SELEX, 1 experiments	best	0.982	0.977	0.868	0.865	0.701	0.729
Non-Methyl HT-SELEX, 1 experiments	median	0.989	0.98	0.98	0.969	0.96	0.945
Non-Methyl HT-SELEX, 1 experiments	best	0.989	0.98	0.98	0.969	0.96	0.945

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.724	0.529	0.648	0.429

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.1.M.D.pcm
PWM	CDX4.H12INVIVO.1.M.D.pwm
PFM	CDX4.H12INVIVO.1.M.D.pfm
Alignment	CDX4.H12INVIVO.1.M.D.words.tsv
Threshold to P-value map	CDX4.H12INVIVO.1.M.D.thr
Motif in other formats
JASPAR format	CDX4.H12INVIVO.1.M.D_jaspar_format.txt
MEME format	CDX4.H12INVIVO.1.M.D_meme_format.meme
Transfac format	CDX4.H12INVIVO.1.M.D_transfac_format.txt
Homer format	CDX4.H12INVIVO.1.M.D_homer_format_0.001.txt CDX4.H12INVIVO.1.M.D_homer_format_0.0005.txt CDX4.H12INVIVO.1.M.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1400.0	2078.0	2401.0	977.0
02	1339.0	584.0	1359.0	3574.0
03	33.0	11.0	14.0	6798.0
04	0.0	0.0	0.0	6856.0
05	0.0	0.0	0.0	6856.0
06	6856.0	0.0	0.0	0.0
07	0.0	5427.0	2.0	1427.0
08	9.0	4.0	6511.0	332.0
09	6543.0	15.0	291.0	7.0
10	26.0	5332.0	322.0	1176.0
11	1081.0	3074.0	2199.0	502.0
12	598.25	3202.25	1335.25	1720.25
13	901.0	2267.0	1989.0	1699.0

PFM

	A	C	G	T
01	0.204	0.303	0.35	0.143
02	0.195	0.085	0.198	0.521
03	0.005	0.002	0.002	0.992
04	0.0	0.0	0.0	1.0
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	0.0	0.792	0.0	0.208
08	0.001	0.001	0.95	0.048
09	0.954	0.002	0.042	0.001
10	0.004	0.778	0.047	0.172
11	0.158	0.448	0.321	0.073
12	0.087	0.467	0.195	0.251
13	0.131	0.331	0.29	0.248

PWM

	A	C	G	T
01	-0.202	0.192	0.337	-0.561
02	-0.247	-1.074	-0.232	0.734
03	-3.887	-4.867	-4.662	1.377
04	-6.656	-6.656	-6.656	1.385
05	-6.656	-6.656	-6.656	1.385
06	1.385	-6.656	-6.656	-6.656
07	-6.656	1.152	-6.011	-0.183
08	-5.031	-5.622	1.334	-1.636
09	1.339	-4.602	-1.767	-5.228
10	-4.108	1.134	-1.666	-0.376
11	-0.46	0.584	0.249	-1.225
12	-1.05	0.624	-0.249	0.004
13	-0.642	0.279	0.149	-0.009

Standard thresholds

P-value	Threshold
0.001	1.27996
0.0005	2.85226
0.0001	6.47536