HXC8.H12RSNP.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC8.H12RSNP.0.SM.D
Gene (human)	HOXC8 (GeneCards)
Gene synonyms (human)	HOX3A
Gene (mouse)	Hoxc8
Gene synonyms (mouse)	Hox-3.1, Hoxc-8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nhvYTAATGRSbn
GC content	39.58%
Information content (bits; total / per base)	10.667 / 0.821
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9037

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.967	0.945	0.949	0.921	0.9	0.872
Overall, 2 experiments	best	0.968	0.947	0.952	0.924	0.917	0.886
Methyl HT-SELEX, 1 experiments	median	0.966	0.944	0.947	0.918	0.882	0.857
Methyl HT-SELEX, 1 experiments	best	0.966	0.944	0.947	0.918	0.882	0.857
Non-Methyl HT-SELEX, 1 experiments	median	0.968	0.947	0.952	0.924	0.917	0.886
Non-Methyl HT-SELEX, 1 experiments	best	0.968	0.947	0.952	0.924	0.917	0.886

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	HOX8 {3.1.1.7} (TFClass)
TFClass ID	TFClass: 3.1.1.7.2
HGNC	HGNC:5129
MGI	MGI:96198
EntrezGene (human)	GeneID:3224 (SSTAR profile)
EntrezGene (mouse)	GeneID:15426 (SSTAR profile)
UniProt ID (human)	HXC8_HUMAN
UniProt ID (mouse)	HXC8_MOUSE
UniProt AC (human)	P31273 (TFClass)
UniProt AC (mouse)	P09025 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXC8.H12RSNP.0.SM.D.pcm
PWM	HXC8.H12RSNP.0.SM.D.pwm
PFM	HXC8.H12RSNP.0.SM.D.pfm
Alignment	HXC8.H12RSNP.0.SM.D.words.tsv
Threshold to P-value map	HXC8.H12RSNP.0.SM.D.thr
Motif in other formats
JASPAR format	HXC8.H12RSNP.0.SM.D_jaspar_format.txt
MEME format	HXC8.H12RSNP.0.SM.D_meme_format.meme
Transfac format	HXC8.H12RSNP.0.SM.D_transfac_format.txt
Homer format	HXC8.H12RSNP.0.SM.D_homer_format_0.001.txt HXC8.H12RSNP.0.SM.D_homer_format_0.0005.txt HXC8.H12RSNP.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2062.75	2473.75	2267.75	2232.75
02	1827.75	4214.75	1328.75	1665.75
03	2818.0	2667.0	2739.0	813.0
04	1070.0	1267.0	879.0	5821.0
05	10.0	2.0	0.0	9025.0
06	9037.0	0.0	0.0	0.0
07	9037.0	0.0	0.0	0.0
08	1.0	2266.0	0.0	6770.0
09	33.0	8.0	5743.0	3253.0
10	5991.0	24.0	2903.0	119.0
11	289.0	5826.0	1751.0	1171.0
12	1424.0	3712.0	2323.0	1578.0
13	2416.5	2348.5	1757.5	2514.5

PFM

	A	C	G	T
01	0.228	0.274	0.251	0.247
02	0.202	0.466	0.147	0.184
03	0.312	0.295	0.303	0.09
04	0.118	0.14	0.097	0.644
05	0.001	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	0.251	0.0	0.749
09	0.004	0.001	0.635	0.36
10	0.663	0.003	0.321	0.013
11	0.032	0.645	0.194	0.13
12	0.158	0.411	0.257	0.175
13	0.267	0.26	0.194	0.278

PWM

	A	C	G	T
01	-0.091	0.091	0.004	-0.012
02	-0.212	0.623	-0.53	-0.304
03	0.221	0.166	0.192	-1.02
04	-0.746	-0.578	-0.942	0.946
05	-5.216	-6.27	-6.901	1.384
06	1.386	-6.901	-6.901	-6.901
07	1.386	-6.901	-6.901	-6.901
08	-6.537	0.003	-6.901	1.097
09	-4.161	-5.394	0.932	0.364
10	0.975	-4.455	0.25	-2.926
11	-2.05	0.947	-0.255	-0.656
12	-0.461	0.496	0.028	-0.358
13	0.067	0.039	-0.251	0.107

Standard thresholds

P-value	Threshold
0.001	4.81931
0.0005	5.95836
0.0001	7.62086