HXB5.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB5.H12INVIVO.0.SM.D
Gene (human)	HOXB5 (GeneCards)
Gene synonyms (human)	HOX2A
Gene (mouse)	Hoxb5
Gene synonyms (mouse)	Hox-2.1, Hoxb-5
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	11
Consensus	nvbTAATKRbn
GC content	35.75%
Information content (bits; total / per base)	10.496 / 0.954
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9369

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.869	0.836	0.786	0.762	0.672	0.677
Overall, 6 experiments	best	0.96	0.934	0.933	0.901	0.864	0.836
Methyl HT-SELEX, 2 experiments	median	0.877	0.847	0.805	0.782	0.73	0.718
Methyl HT-SELEX, 2 experiments	best	0.96	0.934	0.933	0.901	0.864	0.836
Non-Methyl HT-SELEX, 4 experiments	median	0.817	0.78	0.748	0.725	0.654	0.655
Non-Methyl HT-SELEX, 4 experiments	best	0.956	0.934	0.899	0.868	0.804	0.78

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	HOX5 {3.1.1.5} (TFClass)
TFClass ID	TFClass: 3.1.1.5.2
HGNC	HGNC:5116
MGI	MGI:96186
EntrezGene (human)	GeneID:3215 (SSTAR profile)
EntrezGene (mouse)	GeneID:15413 (SSTAR profile)
UniProt ID (human)	HXB5_HUMAN
UniProt ID (mouse)	HXB5_MOUSE
UniProt AC (human)	P09067 (TFClass)
UniProt AC (mouse)	P09079 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	HXB5.H12INVIVO.0.SM.D.pcm
PWM	HXB5.H12INVIVO.0.SM.D.pwm
PFM	HXB5.H12INVIVO.0.SM.D.pfm
Alignment	HXB5.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXB5.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXB5.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXB5.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXB5.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXB5.H12INVIVO.0.SM.D_homer_format_0.001.txt HXB5.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXB5.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1907.75	3457.75	1944.75	2058.75
02	2427.0	2313.0	4050.0	579.0
03	316.0	3598.0	1269.0	4186.0
04	0.0	0.0	0.0	9369.0
05	9369.0	0.0	0.0	0.0
06	9369.0	0.0	0.0	0.0
07	0.0	69.0	0.0	9300.0
08	17.0	123.0	4609.0	4620.0
09	5756.0	141.0	3185.0	287.0
10	930.5	4019.5	2765.5	1653.5
11	1850.5	2659.5	2642.5	2216.5

PFM

	A	C	G	T
01	0.204	0.369	0.208	0.22
02	0.259	0.247	0.432	0.062
03	0.034	0.384	0.135	0.447
04	0.0	0.0	0.0	1.0
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.007	0.0	0.993
08	0.002	0.013	0.492	0.493
09	0.614	0.015	0.34	0.031
10	0.099	0.429	0.295	0.176
11	0.198	0.284	0.282	0.237

PWM

	A	C	G	T
01	-0.205	0.389	-0.186	-0.129
02	0.036	-0.013	0.547	-1.395
03	-1.997	0.429	-0.612	0.58
04	-6.933	-6.933	-6.933	1.386
05	1.386	-6.933	-6.933	-6.933
06	1.386	-6.933	-6.933	-6.933
07	-6.933	-3.493	-6.933	1.378
08	-4.8	-2.929	0.676	0.679
09	0.899	-2.795	0.307	-2.092
10	-0.922	0.54	0.166	-0.348
11	-0.235	0.127	0.121	-0.055

Standard thresholds

P-value	Threshold
0.001	4.53474
0.0005	6.09241
0.0001	7.81368