VSX1.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX1.H12RSNP.1.SM.B
Gene (human)	VSX1 (GeneCards)
Gene synonyms (human)	RINX
Gene (mouse)	Vsx1
Gene synonyms (mouse)	Rinx
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	18
Consensus	hWWdddvYTAATTARbnn
GC content	28.05%
Information content (bits; total / per base)	14.597 / 0.811
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2309

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.988	0.979	0.981	0.969	0.952	0.932
Overall, 10 experiments	best	0.994	0.99	0.991	0.985	0.981	0.973
Methyl HT-SELEX, 2 experiments	median	0.977	0.96	0.971	0.951	0.953	0.931
Methyl HT-SELEX, 2 experiments	best	0.994	0.99	0.991	0.985	0.981	0.973
Non-Methyl HT-SELEX, 8 experiments	median	0.988	0.979	0.981	0.969	0.952	0.932
Non-Methyl HT-SELEX, 8 experiments	best	0.993	0.989	0.987	0.979	0.972	0.96

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.916	0.101	0.866	0.483
batch 2	0.86	0.688	0.805	0.608

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.1.SM.B.pcm
PWM	VSX1.H12RSNP.1.SM.B.pwm
PFM	VSX1.H12RSNP.1.SM.B.pfm
Alignment	VSX1.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	VSX1.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	VSX1.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	VSX1.H12RSNP.1.SM.B_meme_format.meme
Transfac format	VSX1.H12RSNP.1.SM.B_transfac_format.txt
Homer format	VSX1.H12RSNP.1.SM.B_homer_format_0.001.txt VSX1.H12RSNP.1.SM.B_homer_format_0.0005.txt VSX1.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	821.25	325.25	251.25	911.25
02	1130.75	125.75	181.75	870.75
03	1296.0	141.0	205.0	667.0
04	666.0	212.0	215.0	1216.0
05	434.0	299.0	336.0	1240.0
06	1143.0	372.0	420.0	374.0
07	990.0	334.0	754.0	231.0
08	14.0	1239.0	243.0	813.0
09	0.0	380.0	0.0	1929.0
10	2307.0	2.0	0.0	0.0
11	2309.0	0.0	0.0	0.0
12	0.0	0.0	0.0	2309.0
13	0.0	3.0	4.0	2302.0
14	2203.0	0.0	106.0	0.0
15	634.0	473.0	1166.0	36.0
16	222.0	1141.0	294.0	652.0
17	337.25	710.25	551.25	710.25
18	470.25	747.25	428.25	663.25

PFM

	A	C	G	T
01	0.356	0.141	0.109	0.395
02	0.49	0.054	0.079	0.377
03	0.561	0.061	0.089	0.289
04	0.288	0.092	0.093	0.527
05	0.188	0.129	0.146	0.537
06	0.495	0.161	0.182	0.162
07	0.429	0.145	0.327	0.1
08	0.006	0.537	0.105	0.352
09	0.0	0.165	0.0	0.835
10	0.999	0.001	0.0	0.0
11	1.0	0.0	0.0	0.0
12	0.0	0.0	0.0	1.0
13	0.0	0.001	0.002	0.997
14	0.954	0.0	0.046	0.0
15	0.275	0.205	0.505	0.016
16	0.096	0.494	0.127	0.282
17	0.146	0.308	0.239	0.308
18	0.204	0.324	0.185	0.287

PWM

	A	C	G	T
01	0.352	-0.571	-0.827	0.455
02	0.671	-1.512	-1.148	0.41
03	0.807	-1.399	-1.029	0.144
04	0.143	-0.996	-0.982	0.743
05	-0.284	-0.655	-0.539	0.763
06	0.681	-0.438	-0.317	-0.432
07	0.538	-0.545	0.266	-0.911
08	-3.593	0.762	-0.861	0.341
09	-5.701	-0.416	-5.701	1.204
10	1.383	-4.991	-5.701	-5.701
11	1.384	-5.701	-5.701	-5.701
12	-5.701	-5.701	-5.701	1.384
13	-5.701	-4.765	-4.581	1.381
14	1.337	-5.701	-1.68	-5.701
15	0.093	-0.198	0.701	-2.726
16	-0.95	0.68	-0.671	0.121
17	-0.535	0.207	-0.046	0.207
18	-0.204	0.257	-0.297	0.138

Standard thresholds

P-value	Threshold
0.001	1.82031
0.0005	3.35286
0.0001	6.76811