HXB7.H12RSNP.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB7.H12RSNP.1.SM.D
Gene (human)	HOXB7 (GeneCards)
Gene synonyms (human)	HOX2C
Gene (mouse)	Hoxb7
Gene synonyms (mouse)	Hox-2.3, Hoxb-7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	11
Consensus	nvbTAATKvbn
GC content	38.34%
Information content (bits; total / per base)	8.447 / 0.768
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9377

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 (7)	0.438	0.467	0.313	0.322	0.45	0.467	0.828	0.853	0	0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.869	0.828	0.807	0.773	0.742	0.72
Overall, 4 experiments	best	0.972	0.955	0.949	0.924	0.895	0.869
Methyl HT-SELEX, 2 experiments	median	0.868	0.833	0.812	0.785	0.749	0.732
Methyl HT-SELEX, 2 experiments	best	0.972	0.955	0.949	0.924	0.895	0.869
Non-Methyl HT-SELEX, 2 experiments	median	0.869	0.828	0.807	0.773	0.742	0.72
Non-Methyl HT-SELEX, 2 experiments	best	0.948	0.916	0.922	0.883	0.872	0.833

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	HOX6-7 {3.1.1.6} (TFClass)
TFClass ID	TFClass: 3.1.1.6.5
HGNC	HGNC:5118
MGI	MGI:96188
EntrezGene (human)	GeneID:3217 (SSTAR profile)
EntrezGene (mouse)	GeneID:15415 (SSTAR profile)
UniProt ID (human)	HXB7_HUMAN
UniProt ID (mouse)	HXB7_MOUSE
UniProt AC (human)	P09629 (TFClass)
UniProt AC (mouse)	P09024 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	HXB7.H12RSNP.1.SM.D.pcm
PWM	HXB7.H12RSNP.1.SM.D.pwm
PFM	HXB7.H12RSNP.1.SM.D.pfm
Alignment	HXB7.H12RSNP.1.SM.D.words.tsv
Threshold to P-value map	HXB7.H12RSNP.1.SM.D.thr
Motif in other formats
JASPAR format	HXB7.H12RSNP.1.SM.D_jaspar_format.txt
MEME format	HXB7.H12RSNP.1.SM.D_meme_format.meme
Transfac format	HXB7.H12RSNP.1.SM.D_transfac_format.txt
Homer format	HXB7.H12RSNP.1.SM.D_homer_format_0.001.txt HXB7.H12RSNP.1.SM.D_homer_format_0.0005.txt HXB7.H12RSNP.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2166.75	2533.75	2501.75	2174.75
02	1825.0	2803.0	3776.0	973.0
03	821.0	1563.0	2629.0	4364.0
04	29.0	137.0	254.0	8957.0
05	9349.0	0.0	28.0	0.0
06	9377.0	0.0	0.0	0.0
07	0.0	1026.0	533.0	7818.0
08	29.0	240.0	5544.0	3564.0
09	3528.0	1060.0	3749.0	1040.0
10	1217.75	3687.75	2646.75	1824.75
11	2260.5	2575.5	2259.5	2281.5

PFM

	A	C	G	T
01	0.231	0.27	0.267	0.232
02	0.195	0.299	0.403	0.104
03	0.088	0.167	0.28	0.465
04	0.003	0.015	0.027	0.955
05	0.997	0.0	0.003	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.109	0.057	0.834
08	0.003	0.026	0.591	0.38
09	0.376	0.113	0.4	0.111
10	0.13	0.393	0.282	0.195
11	0.241	0.275	0.241	0.243

PWM

	A	C	G	T
01	-0.079	0.078	0.065	-0.075
02	-0.25	0.179	0.476	-0.878
03	-1.047	-0.405	0.115	0.621
04	-4.318	-2.824	-2.214	1.34
05	1.383	-6.934	-4.35	-6.934
06	1.386	-6.934	-6.934	-6.934
07	-6.934	-0.825	-1.478	1.204
08	-4.318	-2.271	0.86	0.419
09	0.408	-0.793	0.469	-0.812
10	-0.654	0.453	0.121	-0.25
11	-0.036	0.094	-0.037	-0.027

Standard thresholds

P-value	Threshold
0.001	5.45002
0.0005	6.16806
0.0001	7.213305