VSX1.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX1.H12RSNP.0.SM.B
Gene (human)	VSX1 (GeneCards)
Gene synonyms (human)	RINX
Gene (mouse)	Vsx1
Gene synonyms (mouse)	Rinx
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	nbYAATTARSn
GC content	35.17%
Information content (bits; total / per base)	11.269 / 1.024
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8514

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.995	0.992	0.987	0.981	0.967	0.953
Overall, 10 experiments	best	0.998	0.996	0.995	0.992	0.984	0.979
Methyl HT-SELEX, 2 experiments	median	0.986	0.976	0.978	0.965	0.962	0.945
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.995	0.992	0.984	0.979
Non-Methyl HT-SELEX, 8 experiments	median	0.995	0.992	0.987	0.981	0.967	0.953
Non-Methyl HT-SELEX, 8 experiments	best	0.997	0.995	0.993	0.99	0.979	0.972

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.947	0.214	0.903	0.483
batch 2	0.867	0.705	0.807	0.609

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	VSX {3.1.3.28} (TFClass)
TFClass ID	TFClass: 3.1.3.28.1
HGNC	HGNC:12723
MGI	MGI:1890816
EntrezGene (human)	GeneID:30813 (SSTAR profile)
EntrezGene (mouse)	GeneID:114889 (SSTAR profile)
UniProt ID (human)	VSX1_HUMAN
UniProt ID (mouse)	VSX1_MOUSE
UniProt AC (human)	Q9NZR4 (TFClass)
UniProt AC (mouse)	Q91V10 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	8
Methyl-HT-SELEX	2

PCM	VSX1.H12RSNP.0.SM.B.pcm
PWM	VSX1.H12RSNP.0.SM.B.pwm
PFM	VSX1.H12RSNP.0.SM.B.pfm
Alignment	VSX1.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	VSX1.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	VSX1.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	VSX1.H12RSNP.0.SM.B_meme_format.meme
Transfac format	VSX1.H12RSNP.0.SM.B_transfac_format.txt
Homer format	VSX1.H12RSNP.0.SM.B_homer_format_0.001.txt VSX1.H12RSNP.0.SM.B_homer_format_0.0005.txt VSX1.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1953.0	2584.0	2422.0	1555.0
02	1142.0	3459.0	2632.0	1281.0
03	216.0	3146.0	189.0	4963.0
04	7477.0	558.0	465.0	14.0
05	8514.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8514.0
07	0.0	0.0	0.0	8514.0
08	8514.0	0.0	0.0	0.0
09	2386.0	965.0	4889.0	274.0
10	259.75	4760.75	1876.75	1616.75
11	1433.75	1997.75	2994.75	2087.75

PFM

	A	C	G	T
01	0.229	0.304	0.284	0.183
02	0.134	0.406	0.309	0.15
03	0.025	0.37	0.022	0.583
04	0.878	0.066	0.055	0.002
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	1.0	0.0	0.0	0.0
09	0.28	0.113	0.574	0.032
10	0.031	0.559	0.22	0.19
11	0.168	0.235	0.352	0.245

PWM

	A	C	G	T
01	-0.086	0.194	0.129	-0.314
02	-0.622	0.485	0.212	-0.507
03	-2.279	0.39	-2.411	0.846
04	1.256	-1.336	-1.517	-4.875
05	1.385	-6.848	-6.848	-6.848
06	-6.848	-6.848	-6.848	1.385
07	-6.848	-6.848	-6.848	1.385
08	1.385	-6.848	-6.848	-6.848
09	0.114	-0.79	0.831	-2.043
10	-2.096	0.804	-0.126	-0.275
11	-0.395	-0.063	0.341	-0.019

Standard thresholds

P-value	Threshold
0.001	4.21213
0.0005	5.55672
0.0001	7.815795