HXC4.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC4.H12INVIVO.0.SM.D
Gene (human)	HOXC4 (GeneCards)
Gene synonyms (human)	HOX3E
Gene (mouse)	Hoxc4
Gene synonyms (mouse)	Hox-3.5, Hoxc-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nbvYTAATKAbbn
GC content	36.04%
Information content (bits; total / per base)	11.786 / 0.907
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9636

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.982	0.969	0.957	0.94	0.849	0.85
Overall, 2 experiments	best	0.983	0.97	0.97	0.953	0.931	0.911
Methyl HT-SELEX, 1 experiments	median	0.981	0.969	0.944	0.926	0.766	0.79
Methyl HT-SELEX, 1 experiments	best	0.981	0.969	0.944	0.926	0.766	0.79
Non-Methyl HT-SELEX, 1 experiments	median	0.983	0.97	0.97	0.953	0.931	0.911
Non-Methyl HT-SELEX, 1 experiments	best	0.983	0.97	0.97	0.953	0.931	0.911

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: 3.1.1.4.3
HGNC	HGNC:5126
MGI	MGI:96195
EntrezGene (human)	GeneID:3221 (SSTAR profile)
EntrezGene (mouse)	GeneID:15423 (SSTAR profile)
UniProt ID (human)	HXC4_HUMAN
UniProt ID (mouse)	HXC4_MOUSE
UniProt AC (human)	P09017 (TFClass)
UniProt AC (mouse)	Q08624 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	HXC4.H12INVIVO.0.SM.D.pcm
PWM	HXC4.H12INVIVO.0.SM.D.pwm
PFM	HXC4.H12INVIVO.0.SM.D.pfm
Alignment	HXC4.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXC4.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXC4.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXC4.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXC4.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXC4.H12INVIVO.0.SM.D_homer_format_0.001.txt HXC4.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXC4.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3225.25	2076.25	2113.25	2221.25
02	1717.25	4318.25	1786.25	1814.25
03	2434.0	2516.0	4328.0	358.0
04	401.0	3988.0	276.0	4971.0
05	0.0	0.0	0.0	9636.0
06	9636.0	0.0	0.0	0.0
07	9636.0	0.0	0.0	0.0
08	0.0	220.0	0.0	9416.0
09	3.0	6.0	5098.0	4529.0
10	8584.0	10.0	1039.0	3.0
11	597.0	4375.0	1748.0	2916.0
12	1489.75	3734.75	2568.75	1842.75
13	2271.5	2742.5	2198.5	2423.5

PFM

	A	C	G	T
01	0.335	0.215	0.219	0.231
02	0.178	0.448	0.185	0.188
03	0.253	0.261	0.449	0.037
04	0.042	0.414	0.029	0.516
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.023	0.0	0.977
09	0.0	0.001	0.529	0.47
10	0.891	0.001	0.108	0.0
11	0.062	0.454	0.181	0.303
12	0.155	0.388	0.267	0.191
13	0.236	0.285	0.228	0.252

PWM

	A	C	G	T
01	0.292	-0.148	-0.131	-0.081
02	-0.338	0.583	-0.299	-0.283
03	0.01	0.043	0.585	-1.901
04	-1.788	0.504	-2.159	0.724
05	-6.958	-6.958	-6.958	1.386
06	1.386	-6.958	-6.958	-6.958
07	1.386	-6.958	-6.958	-6.958
08	-6.958	-2.384	-6.958	1.362
09	-6.121	-5.672	0.749	0.631
10	1.27	-5.279	-0.84	-6.121
11	-1.392	0.596	-0.32	0.191
12	-0.48	0.438	0.064	-0.268
13	-0.059	0.13	-0.091	0.006

Standard thresholds

P-value	Threshold
0.001	3.11931
0.0005	5.18676
0.0001	7.88546