VAX2.H13RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VAX2.H13RSNP.0.SM.B
Gene (human)	VAX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Vax2
Gene synonyms (mouse)	Vex
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	nvbTAATTARbnn
GC content	32.0%
Information content (bits; total / per base)	11.903 / 0.916
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8944
Previous names	VAX2.H12RSNP.0.SM.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.966	0.944	0.939	0.911	0.868	0.829
Overall, 6 experiments	best	0.978	0.961	0.969	0.948	0.952	0.928
Methyl HT-SELEX, 2 experiments	median	0.95	0.917	0.936	0.899	0.911	0.872
Methyl HT-SELEX, 2 experiments	best	0.978	0.961	0.969	0.948	0.952	0.928
Non-Methyl HT-SELEX, 4 experiments	median	0.966	0.944	0.939	0.911	0.86	0.829
Non-Methyl HT-SELEX, 4 experiments	best	0.974	0.954	0.964	0.941	0.949	0.921

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.997	0.972	0.969	0.637
batch 2	0.726	0.569	0.779	0.563

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: 3.1.2.22.2
HGNC	HGNC:12661
MGI	MGI:1346018
EntrezGene (human)	GeneID:25806 (SSTAR profile)
EntrezGene (mouse)	GeneID:24113 (SSTAR profile)
UniProt ID (human)	VAX2_HUMAN
UniProt ID (mouse)	VAX2_MOUSE
UniProt AC (human)	Q9UIW0 (TFClass)
UniProt AC (mouse)	Q9WTP9 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	VAX2.H13RSNP.0.SM.B.pcm
PWM	VAX2.H13RSNP.0.SM.B.pwm
PFM	VAX2.H13RSNP.0.SM.B.pfm
Threshold to P-value map	VAX2.H13RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	VAX2.H13RSNP.0.SM.B_jaspar_format.txt
MEME format	VAX2.H13RSNP.0.SM.B_meme_format.meme
Transfac format	VAX2.H13RSNP.0.SM.B_transfac_format.txt
Homer format	VAX2.H13RSNP.0.SM.B_homer_format_0.001.txt VAX2.H13RSNP.0.SM.B_homer_format_0.0005.txt VAX2.H13RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2599.0	1393.0	2624.0	2328.0
02	2211.75	1801.75	3644.75	1285.75
03	1085.0	3015.0	3655.0	1189.0
04	41.0	679.0	13.0	8211.0
05	6450.0	2474.0	18.0	2.0
06	8944.0	0.0	0.0	0.0
07	0.0	0.0	0.0	8944.0
08	0.0	0.0	0.0	8944.0
09	8943.0	0.0	0.0	1.0
10	4600.0	371.0	3842.0	131.0
11	903.0	2481.0	2049.0	3511.0
12	1649.5	2174.5	3020.5	2099.5
13	2634.25	2240.25	1713.25	2356.25

PFM

	A	C	G	T
01	0.291	0.156	0.293	0.26
02	0.247	0.201	0.408	0.144
03	0.121	0.337	0.409	0.133
04	0.005	0.076	0.001	0.918
05	0.721	0.277	0.002	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	1.0	0.0	0.0	0.0
10	0.514	0.041	0.43	0.015
11	0.101	0.277	0.229	0.393
12	0.184	0.243	0.338	0.235
13	0.295	0.25	0.192	0.263

PWM

	A	C	G	T
01	0.15	-0.473	0.16	0.04
02	-0.011	-0.216	0.488	-0.553
03	-0.722	0.299	0.491	-0.631
04	-3.946	-1.189	-4.987	1.3
05	1.059	0.101	-4.704	-6.261
06	1.386	-6.892	-6.892	-6.892
07	-6.892	-6.892	-6.892	1.386
08	-6.892	-6.892	-6.892	1.386
09	1.385	-6.892	-6.892	-6.527
10	0.721	-1.791	0.541	-2.821
11	-0.905	0.104	-0.087	0.451
12	-0.304	-0.028	0.3	-0.063
13	0.164	0.002	-0.266	0.052

Standard thresholds

P-value	Threshold
0.001	2.63626
0.0005	4.91006
0.0001	7.92157