HMX3.H12RSNP.0.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HMX3.H12RSNP.0.S.B
Gene (human)	HMX3 (GeneCards)
Gene synonyms (human)	NKX-5.1, NKX5-1
Gene (mouse)	Hmx3
Gene synonyms (mouse)	Nkx-5.1, Nkx5-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	nvvTTAATTGvbn
GC content	35.15%
Information content (bits; total / per base)	13.513 / 1.039
Data sources	HT-SELEX
Aligned words	674

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.944	0.916	0.877	0.849	0.745	0.744
Non-Methyl HT-SELEX, 2 experiments	best	0.969	0.951	0.926	0.902	0.785	0.787

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.996	0.771	0.961	0.533
batch 2	0.905	0.147	0.85	0.385

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	NK5-HMX {3.1.2.18} (TFClass)
TFClass ID	TFClass: 3.1.2.18.3
HGNC	HGNC:5019
MGI	MGI:107160
EntrezGene (human)	GeneID:340784 (SSTAR profile)
EntrezGene (mouse)	GeneID:15373 (SSTAR profile)
UniProt ID (human)	HMX3_HUMAN
UniProt ID (mouse)	HMX3_MOUSE
UniProt AC (human)	A6NHT5 (TFClass)
UniProt AC (mouse)	P42581 (TFClass)
GRECO-DB-TF	yes

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

PCM	HMX3.H12RSNP.0.S.B.pcm
PWM	HMX3.H12RSNP.0.S.B.pwm
PFM	HMX3.H12RSNP.0.S.B.pfm
Alignment	HMX3.H12RSNP.0.S.B.words.tsv
Threshold to P-value map	HMX3.H12RSNP.0.S.B.thr
Motif in other formats
JASPAR format	HMX3.H12RSNP.0.S.B_jaspar_format.txt
MEME format	HMX3.H12RSNP.0.S.B_meme_format.meme
Transfac format	HMX3.H12RSNP.0.S.B_transfac_format.txt
Homer format	HMX3.H12RSNP.0.S.B_homer_format_0.001.txt HMX3.H12RSNP.0.S.B_homer_format_0.0005.txt HMX3.H12RSNP.0.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	114.0	212.0	151.0	197.0
02	217.75	162.75	210.75	82.75
03	204.0	247.0	155.0	68.0
04	2.0	18.0	2.0	652.0
05	0.0	2.0	0.0	672.0
06	674.0	0.0	0.0	0.0
07	674.0	0.0	0.0	0.0
08	0.0	0.0	161.0	513.0
09	0.0	10.0	0.0	664.0
10	0.0	0.0	674.0	0.0
11	150.0	281.0	155.0	88.0
12	55.75	234.75	84.75	298.75
13	166.0	210.0	109.0	189.0

PFM

	A	C	G	T
01	0.169	0.315	0.224	0.292
02	0.323	0.241	0.313	0.123
03	0.303	0.366	0.23	0.101
04	0.003	0.027	0.003	0.967
05	0.0	0.003	0.0	0.997
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.239	0.761
09	0.0	0.015	0.0	0.985
10	0.0	0.0	1.0	0.0
11	0.223	0.417	0.23	0.131
12	0.083	0.348	0.126	0.443
13	0.246	0.312	0.162	0.28

PWM

	A	C	G	T
01	-0.386	0.228	-0.109	0.155
02	0.254	-0.034	0.222	-0.701
03	0.19	0.379	-0.083	-0.893
04	-3.848	-2.16	-3.848	1.346
05	-4.649	-3.848	-4.649	1.376
06	1.379	-4.649	-4.649	-4.649
07	1.379	-4.649	-4.649	-4.649
08	-4.649	-4.649	-0.045	1.107
09	-4.649	-2.683	-4.649	1.364
10	-4.649	-4.649	1.379	-4.649
11	-0.115	0.508	-0.083	-0.641
12	-1.087	0.329	-0.678	0.568
13	-0.015	0.218	-0.43	0.114

Standard thresholds

P-value	Threshold
0.001	3.02986
0.0005	3.99016
0.0001	7.178125