VSX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX1.H12INVIVO.0.SM.D
Gene (human)	VSX1 (GeneCards)
Gene synonyms (human)	RINX
Gene (mouse)	Vsx1
Gene synonyms (mouse)	Rinx
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nbTAATTAGCbn
GC content	35.97%
Information content (bits; total / per base)	13.865 / 1.155
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8621

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.996	0.994	0.987	0.982	0.964	0.949
Overall, 10 experiments	best	0.998	0.997	0.995	0.993	0.985	0.98
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	0.997	0.995	0.993	0.985	0.98
Non-Methyl HT-SELEX, 8 experiments	median	0.996	0.994	0.987	0.982	0.964	0.949
Non-Methyl HT-SELEX, 8 experiments	best	0.998	0.996	0.993	0.991	0.979	0.973

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.914	0.165	0.889	0.477
batch 2	0.867	0.722	0.815	0.632

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.0.SM.D.pcm
PWM	VSX1.H12INVIVO.0.SM.D.pwm
PFM	VSX1.H12INVIVO.0.SM.D.pfm
Alignment	VSX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	VSX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	VSX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	VSX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	VSX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	VSX1.H12INVIVO.0.SM.D_homer_format_0.001.txt VSX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt VSX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2001.75	2269.75	2959.75	1389.75
02	824.5	3886.5	1996.5	1913.5
03	60.0	1338.0	41.0	7182.0
04	8437.0	85.0	99.0	0.0
05	8621.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8621.0
07	0.0	0.0	0.0	8621.0
08	8617.0	0.0	4.0	0.0
09	482.0	366.0	7683.0	90.0
10	87.0	6872.0	900.0	762.0
11	1105.5	3279.5	1889.5	2346.5
12	2772.5	2249.5	1291.5	2307.5

PFM

	A	C	G	T
01	0.232	0.263	0.343	0.161
02	0.096	0.451	0.232	0.222
03	0.007	0.155	0.005	0.833
04	0.979	0.01	0.011	0.0
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	0.056	0.042	0.891	0.01
10	0.01	0.797	0.104	0.088
11	0.128	0.38	0.219	0.272
12	0.322	0.261	0.15	0.268

PWM

	A	C	G	T
01	-0.074	0.052	0.317	-0.438
02	-0.959	0.589	-0.076	-0.119
03	-3.545	-0.476	-3.909	1.203
04	1.364	-3.208	-3.059	-6.859
05	1.386	-6.859	-6.859	-6.859
06	-6.859	-6.859	-6.859	1.386
07	-6.859	-6.859	-6.859	1.386
08	1.385	-6.859	-5.842	-6.859
09	-1.494	-1.768	1.27	-3.152
10	-3.185	1.159	-0.872	-1.038
11	-0.667	0.419	-0.131	0.085
12	0.252	0.043	-0.511	0.068

Standard thresholds

P-value	Threshold
0.001	1.746815
0.0005	3.48833
0.0001	6.85368