HXD11.H12CORE.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD11.H12CORE.0.PS.A
Gene (human)	HOXD11 (GeneCards)
Gene synonyms (human)	HOX4F
Gene (mouse)	Hoxd11
Gene synonyms (mouse)	Hox-4.6, Hoxd-11
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	vdRnTTWATGRbb
GC content	37.82%
Information content (bits; total / per base)	10.532 / 0.81
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	1 (7)	0.845	0.855	0.764	0.776	0.866	0.874	3.154	3.193	198.244	208.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.791	0.748	0.741	0.707	0.678	0.659
Overall, 4 experiments	best	0.953	0.923	0.931	0.895	0.878	0.843
Methyl HT-SELEX, 1 experiments	median	0.927	0.887	0.888	0.843	0.803	0.771
Methyl HT-SELEX, 1 experiments	best	0.927	0.887	0.888	0.843	0.803	0.771
Non-Methyl HT-SELEX, 3 experiments	median	0.654	0.609	0.593	0.572	0.552	0.547
Non-Methyl HT-SELEX, 3 experiments	best	0.953	0.923	0.931	0.895	0.878	0.843

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	HOX9-13 {3.1.1.8} (TFClass)
TFClass ID	TFClass: 3.1.1.8.11
HGNC	HGNC:5134
MGI	MGI:96203
EntrezGene (human)	GeneID:3237 (SSTAR profile)
EntrezGene (mouse)	GeneID:15431 (SSTAR profile)
UniProt ID (human)	HXD11_HUMAN
UniProt ID (mouse)	HXD11_MOUSE
UniProt AC (human)	P31277 (TFClass)
UniProt AC (mouse)	P23813 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXD11.H12CORE.0.PS.A.pcm
PWM	HXD11.H12CORE.0.PS.A.pwm
PFM	HXD11.H12CORE.0.PS.A.pfm
Alignment	HXD11.H12CORE.0.PS.A.words.tsv
Threshold to P-value map	HXD11.H12CORE.0.PS.A.thr
Motif in other formats
JASPAR format	HXD11.H12CORE.0.PS.A_jaspar_format.txt
MEME format	HXD11.H12CORE.0.PS.A_meme_format.meme
Transfac format	HXD11.H12CORE.0.PS.A_transfac_format.txt
Homer format	HXD11.H12CORE.0.PS.A_homer_format_0.001.txt HXD11.H12CORE.0.PS.A_homer_format_0.0005.txt HXD11.H12CORE.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	309.0	338.0	241.0	112.0
02	483.0	59.0	204.0	254.0
03	274.0	69.0	592.0	65.0
04	292.0	164.0	220.0	324.0
05	9.0	3.0	38.0	950.0
06	10.0	9.0	6.0	975.0
07	445.0	46.0	28.0	481.0
08	969.0	10.0	20.0	1.0
09	5.0	45.0	8.0	942.0
10	25.0	22.0	770.0	183.0
11	410.0	8.0	501.0	81.0
12	104.0	367.0	381.0	148.0
13	83.0	511.0	257.0	149.0

PFM

	A	C	G	T
01	0.309	0.338	0.241	0.112
02	0.483	0.059	0.204	0.254
03	0.274	0.069	0.592	0.065
04	0.292	0.164	0.22	0.324
05	0.009	0.003	0.038	0.95
06	0.01	0.009	0.006	0.975
07	0.445	0.046	0.028	0.481
08	0.969	0.01	0.02	0.001
09	0.005	0.045	0.008	0.942
10	0.025	0.022	0.77	0.183
11	0.41	0.008	0.501	0.081
12	0.104	0.367	0.381	0.148
13	0.083	0.511	0.257	0.149

PWM

	A	C	G	T
01	0.211	0.3	-0.036	-0.795
02	0.655	-1.422	-0.202	0.016
03	0.091	-1.27	0.858	-1.328
04	0.154	-0.418	-0.127	0.258
05	-3.156	-3.975	-1.846	1.33
06	-3.066	-3.156	-3.484	1.356
07	0.574	-1.663	-2.136	0.651
08	1.35	-3.066	-2.45	-4.525
09	-3.622	-1.684	-3.253	1.321
10	-2.243	-2.362	1.12	-0.309
11	0.492	-3.253	0.692	-1.113
12	-0.867	0.382	0.419	-0.52
13	-1.089	0.711	0.027	-0.513

Standard thresholds

P-value	Threshold
0.001	4.58601
0.0005	5.52306
0.0001	7.44701