HXB8.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB8.H12INVIVO.0.PSM.A
Gene (human)	HOXB8 (GeneCards)
Gene synonyms (human)	HOX2D
Gene (mouse)	Hoxb8
Gene synonyms (mouse)	Hox-2.4, Hoxb-8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	hYKWATGRSW
GC content	33.93%
Information content (bits; total / per base)	9.392 / 0.939
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	993

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
Human	1 (5)	0.807	0.835	0.658	0.682	0.723	0.729	1.841	1.912	39.081	42.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.89	0.836	0.838	0.786	0.766	0.727
Overall, 2 experiments	best	0.917	0.871	0.874	0.825	0.804	0.763
Methyl HT-SELEX, 1 experiments	median	0.862	0.801	0.802	0.747	0.729	0.69
Methyl HT-SELEX, 1 experiments	best	0.862	0.801	0.802	0.747	0.729	0.69
Non-Methyl HT-SELEX, 1 experiments	median	0.917	0.871	0.874	0.825	0.804	0.763
Non-Methyl HT-SELEX, 1 experiments	best	0.917	0.871	0.874	0.825	0.804	0.763

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: 3.1.1.7.1
HGNC	HGNC:5119
MGI	MGI:96189
EntrezGene (human)	GeneID:3218 (SSTAR profile)
EntrezGene (mouse)	GeneID:15416 (SSTAR profile)
UniProt ID (human)	HXB8_HUMAN
UniProt ID (mouse)	HXB8_MOUSE
UniProt AC (human)	P17481 (TFClass)
UniProt AC (mouse)	P09632 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXB8.H12INVIVO.0.PSM.A.pcm
PWM	HXB8.H12INVIVO.0.PSM.A.pwm
PFM	HXB8.H12INVIVO.0.PSM.A.pfm
Alignment	HXB8.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	HXB8.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	HXB8.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	HXB8.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	HXB8.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	HXB8.H12INVIVO.0.PSM.A_homer_format_0.001.txt HXB8.H12INVIVO.0.PSM.A_homer_format_0.0005.txt HXB8.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	185.0	281.0	108.0	419.0
02	76.0	142.0	26.0	749.0
03	81.0	28.0	98.0	786.0
04	676.0	27.0	30.0	260.0
05	922.0	15.0	52.0	4.0
06	6.0	4.0	16.0	967.0
07	32.0	3.0	736.0	222.0
08	210.0	22.0	735.0	26.0
09	102.0	744.0	104.0	43.0
10	331.0	193.0	5.0	464.0

PFM

	A	C	G	T
01	0.186	0.283	0.109	0.422
02	0.077	0.143	0.026	0.754
03	0.082	0.028	0.099	0.792
04	0.681	0.027	0.03	0.262
05	0.928	0.015	0.052	0.004
06	0.006	0.004	0.016	0.974
07	0.032	0.003	0.741	0.224
08	0.211	0.022	0.74	0.026
09	0.103	0.749	0.105	0.043
10	0.333	0.194	0.005	0.467

PWM

	A	C	G	T
01	-0.292	0.123	-0.823	0.521
02	-1.168	-0.553	-2.199	1.1
03	-1.106	-2.129	-0.919	1.148
04	0.997	-2.164	-2.064	0.046
05	1.307	-2.704	-1.537	-3.776
06	-3.477	-3.776	-2.646	1.355
07	-2.003	-3.968	1.082	-0.111
08	-0.166	-2.355	1.081	-2.199
09	-0.88	1.093	-0.861	-1.721
10	0.286	-0.25	-3.616	0.622

Standard thresholds

P-value	Threshold
0.001	4.878755
0.0005	5.6997
0.0001	7.244495