HXB4.H13CORE.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB4.H13CORE.1.PSM.A
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	1
Quality	A

Motif length	13
Consensus	nnvYTAATKAbnn
GC content	36.35%
Information content (bits; total / per base)	11.029 / 0.848
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9826
Previous names	HXB4.H12CORE.1.PSM.A

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)	0.7	0.74	0.569	0.59	0.674	0.743	1.958	2.137	135.959	198.119

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.951	0.928	0.874	0.856	0.771	0.771
Overall, 2 experiments	best	0.972	0.954	0.953	0.929	0.893	0.869
Methyl HT-SELEX, 1 experiments	median	0.93	0.903	0.795	0.784	0.649	0.673
Methyl HT-SELEX, 1 experiments	best	0.93	0.903	0.795	0.784	0.649	0.673
Non-Methyl HT-SELEX, 1 experiments	median	0.972	0.954	0.953	0.929	0.893	0.869
Non-Methyl HT-SELEX, 1 experiments	best	0.972	0.954	0.953	0.929	0.893	0.869

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	HXB4.H13CORE.1.PSM.A.pcm
PWM	HXB4.H13CORE.1.PSM.A.pwm
PFM	HXB4.H13CORE.1.PSM.A.pfm
Threshold to P-value map	HXB4.H13CORE.1.PSM.A.thr
Motif in other formats
JASPAR format	HXB4.H13CORE.1.PSM.A_jaspar_format.txt
MEME format	HXB4.H13CORE.1.PSM.A_meme_format.meme
Transfac format	HXB4.H13CORE.1.PSM.A_transfac_format.txt
Homer format	HXB4.H13CORE.1.PSM.A_homer_format_0.001.txt HXB4.H13CORE.1.PSM.A_homer_format_0.0005.txt HXB4.H13CORE.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3369.25	1949.25	2413.25	2094.25
02	1789.75	3793.75	2228.75	2013.75
03	2278.0	2399.0	4796.0	353.0
04	413.0	3865.0	662.0	4886.0
05	0.0	3.0	13.0	9810.0
06	9821.0	0.0	5.0	0.0
07	9825.0	0.0	1.0	0.0
08	1.0	523.0	12.0	9290.0
09	8.0	52.0	5565.0	4201.0
10	7929.0	39.0	1791.0	67.0
11	947.0	3555.0	1774.0	3550.0
12	1485.75	3397.75	2667.75	2274.75
13	2313.0	2683.0	2240.0	2590.0

PFM

	A	C	G	T
01	0.343	0.198	0.246	0.213
02	0.182	0.386	0.227	0.205
03	0.232	0.244	0.488	0.036
04	0.042	0.393	0.067	0.497
05	0.0	0.0	0.001	0.998
06	0.999	0.0	0.001	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.053	0.001	0.945
09	0.001	0.005	0.566	0.428
10	0.807	0.004	0.182	0.007
11	0.096	0.362	0.181	0.361
12	0.151	0.346	0.271	0.232
13	0.235	0.273	0.228	0.264

PWM

	A	C	G	T
01	0.316	-0.231	-0.018	-0.159
02	-0.316	0.434	-0.097	-0.199
03	-0.075	-0.024	0.669	-1.934
04	-1.778	0.453	-1.309	0.687
05	-6.975	-6.14	-5.08	1.384
06	1.385	-6.975	-5.82	-6.975
07	1.385	-6.975	-6.614	-6.975
08	-6.614	-1.543	-5.147	1.33
09	-5.475	-3.813	0.817	0.536
10	1.171	-4.087	-0.316	-3.569
11	-0.952	0.369	-0.325	0.368
12	-0.502	0.324	0.082	-0.077
13	-0.06	0.088	-0.092	0.053

Standard thresholds

P-value	Threshold
0.001	4.15361
0.0005	5.68571
0.0001	7.84422