VAX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VAX1.H12INVIVO.0.SM.D
Gene (human)	VAX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Vax1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nvYMATTAvbnn
GC content	38.12%
Information content (bits; total / per base)	10.119 / 0.843
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9974

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.978	0.964	0.963	0.943	0.919	0.896
Overall, 4 experiments	best	0.996	0.993	0.988	0.983	0.949	0.94
Methyl HT-SELEX, 1 experiments	median	0.956	0.926	0.938	0.903	0.906	0.867
Methyl HT-SELEX, 1 experiments	best	0.956	0.926	0.938	0.903	0.906	0.867
Non-Methyl HT-SELEX, 3 experiments	median	0.991	0.986	0.979	0.97	0.927	0.914
Non-Methyl HT-SELEX, 3 experiments	best	0.996	0.993	0.988	0.983	0.949	0.94

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.799	0.673	0.806	0.613

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	VAX {3.1.2.22} (TFClass)
TFClass ID	TFClass: 3.1.2.22.1
HGNC	HGNC:12660
MGI	MGI:1277163
EntrezGene (human)	GeneID:11023 (SSTAR profile)
EntrezGene (mouse)	GeneID:22326 (SSTAR profile)
UniProt ID (human)	VAX1_HUMAN
UniProt ID (mouse)	VAX1_MOUSE
UniProt AC (human)	Q5SQQ9 (TFClass)
UniProt AC (mouse)	Q2NKI2 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	VAX1.H12INVIVO.0.SM.D.pcm
PWM	VAX1.H12INVIVO.0.SM.D.pwm
PFM	VAX1.H12INVIVO.0.SM.D.pfm
Alignment	VAX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	VAX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	VAX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	VAX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	VAX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	VAX1.H12INVIVO.0.SM.D_homer_format_0.001.txt VAX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt VAX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2193.75	3160.75	2880.75	1738.75
02	1718.5	3348.5	3550.5	1356.5
03	370.0	2524.0	211.0	6869.0
04	4453.0	4906.0	471.0	144.0
05	9907.0	29.0	38.0	0.0
06	0.0	2.0	0.0	9972.0
07	0.0	19.0	2.0	9953.0
08	9873.0	1.0	63.0	37.0
09	3261.0	1792.0	4634.0	287.0
10	663.0	4214.0	2642.0	2455.0
11	1648.0	2521.0	3592.0	2213.0
12	2433.75	2789.75	2237.75	2512.75

PFM

	A	C	G	T
01	0.22	0.317	0.289	0.174
02	0.172	0.336	0.356	0.136
03	0.037	0.253	0.021	0.689
04	0.446	0.492	0.047	0.014
05	0.993	0.003	0.004	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.002	0.0	0.998
08	0.99	0.0	0.006	0.004
09	0.327	0.18	0.465	0.029
10	0.066	0.422	0.265	0.246
11	0.165	0.253	0.36	0.222
12	0.244	0.28	0.224	0.252

PWM

	A	C	G	T
01	-0.128	0.237	0.144	-0.36
02	-0.372	0.295	0.353	-0.608
03	-1.903	0.012	-2.46	1.013
04	0.579	0.676	-1.663	-2.837
05	1.379	-4.379	-4.126	-6.989
06	-6.989	-6.363	-6.989	1.385
07	-6.989	-4.764	-6.363	1.383
08	1.375	-6.628	-3.643	-4.151
09	0.268	-0.33	0.619	-2.155
10	-1.322	0.524	0.058	-0.016
11	-0.414	0.011	0.365	-0.119
12	-0.024	0.112	-0.108	0.008

Standard thresholds

P-value	Threshold
0.001	4.82431
0.0005	6.08096
0.0001	7.72564