HXB4.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB4.H12INVIVO.0.P.B
Gene (human)	HOXB4 (GeneCards)
Gene synonyms (human)	HOX2F
Gene (mouse)	Hoxb4
Gene synonyms (mouse)	Hox-2.6, Hoxb-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	9
Consensus	TGAYKRATK
GC content	33.01%
Information content (bits; total / per base)	8.922 / 0.991
Data sources	ChIP-Seq
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	3 (21)	0.742	0.802	0.638	0.727	0.739	0.789	2.343	2.902	223.959	311.076

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.75	0.681	0.688	0.642	0.625	0.603
Overall, 2 experiments	best	0.813	0.732	0.761	0.697	0.694	0.652
Methyl HT-SELEX, 1 experiments	median	0.687	0.63	0.615	0.588	0.557	0.555
Methyl HT-SELEX, 1 experiments	best	0.687	0.63	0.615	0.588	0.557	0.555
Non-Methyl HT-SELEX, 1 experiments	median	0.813	0.732	0.761	0.697	0.694	0.652
Non-Methyl HT-SELEX, 1 experiments	best	0.813	0.732	0.761	0.697	0.694	0.652

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: 3.1.1.4.2
HGNC	HGNC:5115
MGI	MGI:96185
EntrezGene (human)	GeneID:3214 (SSTAR profile)
EntrezGene (mouse)	GeneID:15412 (SSTAR profile)
UniProt ID (human)	HXB4_HUMAN
UniProt ID (mouse)	HXB4_MOUSE
UniProt AC (human)	P17483 (TFClass)
UniProt AC (mouse)	P10284 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXB4.H12INVIVO.0.P.B.pcm
PWM	HXB4.H12INVIVO.0.P.B.pwm
PFM	HXB4.H12INVIVO.0.P.B.pfm
Alignment	HXB4.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	HXB4.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	HXB4.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	HXB4.H12INVIVO.0.P.B_meme_format.meme
Transfac format	HXB4.H12INVIVO.0.P.B_transfac_format.txt
Homer format	HXB4.H12INVIVO.0.P.B_homer_format_0.001.txt HXB4.H12INVIVO.0.P.B_homer_format_0.0005.txt HXB4.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	91.0	7.0	25.0	877.0
02	218.0	9.0	760.0	13.0
03	934.0	48.0	14.0	4.0
04	18.0	166.0	60.0	756.0
05	156.0	9.0	300.0	535.0
06	419.0	22.0	511.0	48.0
07	720.0	270.0	5.0	5.0
08	44.0	39.0	32.0	885.0
09	101.0	81.0	613.0	205.0

PFM

	A	C	G	T
01	0.091	0.007	0.025	0.877
02	0.218	0.009	0.76	0.013
03	0.934	0.048	0.014	0.004
04	0.018	0.166	0.06	0.756
05	0.156	0.009	0.3	0.535
06	0.419	0.022	0.511	0.048
07	0.72	0.27	0.005	0.005
08	0.044	0.039	0.032	0.885
09	0.101	0.081	0.613	0.205

PWM

	A	C	G	T
01	-0.999	-3.362	-2.243	1.25
02	-0.136	-3.156	1.107	-2.839
03	1.313	-1.622	-2.773	-3.783
04	-2.546	-0.406	-1.406	1.102
05	-0.467	-3.156	0.181	0.757
06	0.514	-2.362	0.711	-1.622
07	1.053	0.076	-3.622	-3.622
08	-1.706	-1.821	-2.01	1.259
09	-0.896	-1.113	0.893	-0.197

Standard thresholds

P-value	Threshold
0.001	4.92948
0.0005	5.737735
0.0001	7.23583