HXD3.H12RSNP.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD3.H12RSNP.0.SM.D
Gene (human)	HOXD3 (GeneCards)
Gene synonyms (human)	HOX1D, HOX4A
Gene (mouse)	Hoxd3
Gene synonyms (mouse)	Hox-4.1, Hoxd-3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nbvCTAATTASvn
GC content	40.58%
Information content (bits; total / per base)	13.597 / 1.046
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8662

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.949	0.928	0.886	0.872	0.813	0.814
Overall, 4 experiments	best	0.997	0.996	0.994	0.991	0.984	0.978
Methyl HT-SELEX, 1 experiments	median	0.997	0.996	0.994	0.991	0.984	0.978
Methyl HT-SELEX, 1 experiments	best	0.997	0.996	0.994	0.991	0.984	0.978
Non-Methyl HT-SELEX, 3 experiments	median	0.902	0.864	0.781	0.759	0.65	0.662
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.993	0.99	0.985	0.976	0.967

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	HOX3 {3.1.1.3} (TFClass)
TFClass ID	TFClass: 3.1.1.3.3
HGNC	HGNC:5137
MGI	MGI:96207
EntrezGene (human)	GeneID:3232 (SSTAR profile)
EntrezGene (mouse)	GeneID:15434 (SSTAR profile)
UniProt ID (human)	HXD3_HUMAN
UniProt ID (mouse)	HXD3_MOUSE
UniProt AC (human)	P31249 (TFClass)
UniProt AC (mouse)	P09027 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	HXD3.H12RSNP.0.SM.D.pcm
PWM	HXD3.H12RSNP.0.SM.D.pwm
PFM	HXD3.H12RSNP.0.SM.D.pfm
Alignment	HXD3.H12RSNP.0.SM.D.words.tsv
Threshold to P-value map	HXD3.H12RSNP.0.SM.D.thr
Motif in other formats
JASPAR format	HXD3.H12RSNP.0.SM.D_jaspar_format.txt
MEME format	HXD3.H12RSNP.0.SM.D_meme_format.meme
Transfac format	HXD3.H12RSNP.0.SM.D_transfac_format.txt
Homer format	HXD3.H12RSNP.0.SM.D_homer_format_0.001.txt HXD3.H12RSNP.0.SM.D_homer_format_0.0005.txt HXD3.H12RSNP.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2135.0	2016.0	2481.0	2030.0
02	965.5	4866.5	1322.5	1507.5
03	2241.0	1943.0	4313.0	165.0
04	43.0	6967.0	147.0	1505.0
05	0.0	0.0	0.0	8662.0
06	8662.0	0.0	0.0	0.0
07	8662.0	0.0	0.0	0.0
08	0.0	18.0	0.0	8644.0
09	0.0	6.0	1951.0	6705.0
10	7937.0	4.0	709.0	12.0
11	317.0	5432.0	2369.0	544.0
12	1222.5	4176.5	2106.5	1156.5
13	1539.75	3257.75	1604.75	2259.75

PFM

	A	C	G	T
01	0.246	0.233	0.286	0.234
02	0.111	0.562	0.153	0.174
03	0.259	0.224	0.498	0.019
04	0.005	0.804	0.017	0.174
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	0.002	0.0	0.998
09	0.0	0.001	0.225	0.774
10	0.916	0.0	0.082	0.001
11	0.037	0.627	0.273	0.063
12	0.141	0.482	0.243	0.134
13	0.178	0.376	0.185	0.261

PWM

	A	C	G	T
01	-0.014	-0.071	0.136	-0.065
02	-0.806	0.809	-0.492	-0.362
03	0.034	-0.108	0.688	-2.562
04	-3.869	1.168	-2.676	-0.363
05	-6.863	-6.863	-6.863	1.386
06	1.386	-6.863	-6.863	-6.863
07	1.386	-6.863	-6.863	-6.863
08	-6.863	-4.672	-6.863	1.383
09	-6.863	-5.569	-0.104	1.129
10	1.298	-5.846	-1.114	-5.024
11	-1.915	0.919	0.09	-1.378
12	-0.571	0.656	-0.028	-0.626
13	-0.341	0.408	-0.299	0.043

Standard thresholds

P-value	Threshold
0.001	1.609715
0.0005	3.47836
0.0001	7.194335