HXD4.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD4.H12INVIVO.0.SM.D
Gene (human)	HOXD4 (GeneCards)
Gene synonyms (human)	HOX4B
Gene (mouse)	Hoxd4
Gene synonyms (mouse)	Hox-4.2, Hoxd-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nnvbTAATKRbn
GC content	37.97%
Information content (bits; total / per base)	10.367 / 0.864
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9383

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.95	0.919	0.928	0.89	0.852	0.828
Overall, 4 experiments	best	0.97	0.952	0.938	0.913	0.881	0.845
Methyl HT-SELEX, 2 experiments	median	0.888	0.85	0.813	0.785	0.739	0.724
Methyl HT-SELEX, 2 experiments	best	0.947	0.913	0.926	0.886	0.872	0.835
Non-Methyl HT-SELEX, 2 experiments	median	0.961	0.938	0.934	0.904	0.856	0.833
Non-Methyl HT-SELEX, 2 experiments	best	0.97	0.952	0.938	0.913	0.881	0.845

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	HOX4 {3.1.1.4} (TFClass)
TFClass ID	TFClass: 3.1.1.4.4
HGNC	HGNC:5138
MGI	MGI:96208
EntrezGene (human)	GeneID:3233 (SSTAR profile)
EntrezGene (mouse)	GeneID:15436 (SSTAR profile)
UniProt ID (human)	HXD4_HUMAN
UniProt ID (mouse)	HXD4_MOUSE
UniProt AC (human)	P09016 (TFClass)
UniProt AC (mouse)	P10628 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	HXD4.H12INVIVO.0.SM.D.pcm
PWM	HXD4.H12INVIVO.0.SM.D.pwm
PFM	HXD4.H12INVIVO.0.SM.D.pfm
Alignment	HXD4.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXD4.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXD4.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXD4.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXD4.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXD4.H12INVIVO.0.SM.D_homer_format_0.001.txt HXD4.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXD4.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2389.25	2151.25	2473.25	2369.25
02	1930.0	3726.0	2014.0	1713.0
03	2177.0	2471.0	4298.0	437.0
04	371.0	3692.0	1061.0	4259.0
05	2.0	4.0	1.0	9376.0
06	9383.0	0.0	0.0	0.0
07	9383.0	0.0	0.0	0.0
08	0.0	870.0	0.0	8513.0
09	3.0	136.0	6304.0	2940.0
10	6632.0	171.0	2353.0	227.0
11	1086.0	3433.0	1997.0	2867.0
12	1773.5	2747.5	2854.5	2007.5

PFM

	A	C	G	T
01	0.255	0.229	0.264	0.253
02	0.206	0.397	0.215	0.183
03	0.232	0.263	0.458	0.047
04	0.04	0.393	0.113	0.454
05	0.0	0.0	0.0	0.999
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.093	0.0	0.907
09	0.0	0.014	0.672	0.313
10	0.707	0.018	0.251	0.024
11	0.116	0.366	0.213	0.306
12	0.189	0.293	0.304	0.214

PWM

	A	C	G	T
01	0.018	-0.086	0.053	0.01
02	-0.195	0.462	-0.152	-0.314
03	-0.075	0.052	0.605	-1.676
04	-1.839	0.453	-0.792	0.596
05	-6.306	-5.923	-6.571	1.385
06	1.386	-6.934	-6.934	-6.934
07	1.386	-6.934	-6.934	-6.934
08	-6.934	-0.99	-6.934	1.288
09	-6.096	-2.832	0.988	0.226
10	1.039	-2.606	0.003	-2.326
11	-0.769	0.381	-0.161	0.2
12	-0.279	0.158	0.196	-0.156

Standard thresholds

P-value	Threshold
0.001	4.82506
0.0005	5.96312
0.0001	7.739225