VSX1.H12INVIVO.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX1.H12INVIVO.1.SM.D
Gene (human)	VSX1 (GeneCards)
Gene synonyms (human)	RINX
Gene (mouse)	Vsx1
Gene synonyms (mouse)	Rinx
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	17
Consensus	nvSTAATTAGYhMWWhd
GC content	30.96%
Information content (bits; total / per base)	16.689 / 0.982
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	1689

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.993	0.989	0.986	0.979	0.958	0.941
Overall, 10 experiments	best	0.997	0.995	0.994	0.99	0.984	0.978
Methyl HT-SELEX, 2 experiments	median	0.982	0.969	0.975	0.959	0.958	0.939
Methyl HT-SELEX, 2 experiments	best	0.997	0.995	0.994	0.99	0.984	0.978
Non-Methyl HT-SELEX, 8 experiments	median	0.993	0.989	0.986	0.979	0.958	0.941
Non-Methyl HT-SELEX, 8 experiments	best	0.996	0.994	0.99	0.985	0.977	0.966

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.927	0.083	0.909	0.494
batch 2	0.877	0.728	0.785	0.566

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.H12INVIVO.1.SM.D.pcm
PWM	VSX1.H12INVIVO.1.SM.D.pwm
PFM	VSX1.H12INVIVO.1.SM.D.pfm
Alignment	VSX1.H12INVIVO.1.SM.D.words.tsv
Threshold to P-value map	VSX1.H12INVIVO.1.SM.D.thr
Motif in other formats
JASPAR format	VSX1.H12INVIVO.1.SM.D_jaspar_format.txt
MEME format	VSX1.H12INVIVO.1.SM.D_meme_format.meme
Transfac format	VSX1.H12INVIVO.1.SM.D_transfac_format.txt
Homer format	VSX1.H12INVIVO.1.SM.D_homer_format_0.001.txt VSX1.H12INVIVO.1.SM.D_homer_format_0.0005.txt VSX1.H12INVIVO.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	401.25	532.25	496.25	259.25
02	357.25	305.25	902.25	124.25
03	89.0	1068.0	292.0	240.0
04	1.0	46.0	0.0	1642.0
05	1689.0	0.0	0.0	0.0
06	1689.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1689.0
08	0.0	0.0	0.0	1689.0
09	1620.0	0.0	69.0	0.0
10	283.0	87.0	1318.0	1.0
11	32.0	1109.0	68.0	480.0
12	244.0	618.0	84.0	743.0
13	1156.0	237.0	108.0	188.0
14	983.0	181.0	81.0	444.0
15	301.0	178.0	105.0	1105.0
16	488.0	201.0	156.0	844.0
17	665.5	267.5	379.5	376.5

PFM

	A	C	G	T
01	0.238	0.315	0.294	0.153
02	0.212	0.181	0.534	0.074
03	0.053	0.632	0.173	0.142
04	0.001	0.027	0.0	0.972
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.959	0.0	0.041	0.0
10	0.168	0.052	0.78	0.001
11	0.019	0.657	0.04	0.284
12	0.144	0.366	0.05	0.44
13	0.684	0.14	0.064	0.111
14	0.582	0.107	0.048	0.263
15	0.178	0.105	0.062	0.654
16	0.289	0.119	0.092	0.5
17	0.394	0.158	0.225	0.223

PWM

	A	C	G	T
01	-0.051	0.231	0.161	-0.485
02	-0.166	-0.323	0.757	-1.213
03	-1.541	0.925	-0.367	-0.562
04	-5.0	-2.182	-5.431	1.355
05	1.383	-5.431	-5.431	-5.431
06	1.383	-5.431	-5.431	-5.431
07	-5.431	-5.431	-5.431	1.383
08	-5.431	-5.431	-5.431	1.383
09	1.341	-5.431	-1.789	-5.431
10	-0.398	-1.563	1.135	-5.0
11	-2.528	0.963	-1.804	0.128
12	-0.545	0.38	-1.597	0.563
13	1.004	-0.574	-1.351	-0.804
14	0.843	-0.841	-1.633	0.05
15	-0.337	-0.858	-1.378	0.959
16	0.144	-0.737	-0.988	0.69
17	0.453	-0.454	-0.106	-0.114

Standard thresholds

P-value	Threshold
0.001	0.78201
0.0005	2.35326
0.0001	5.71161