VAX2.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VAX2.H12INVIVO.0.SM.D
Gene (human)	VAX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Vax2
Gene synonyms (mouse)	Vex
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nvvTMATTARbbn
GC content	39.14%
Information content (bits; total / per base)	11.954 / 0.92
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9048

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.974	0.959	0.946	0.923	0.875	0.84
Overall, 6 experiments	best	0.987	0.977	0.978	0.964	0.958	0.939
Methyl HT-SELEX, 2 experiments	median	0.963	0.939	0.947	0.918	0.917	0.886
Methyl HT-SELEX, 2 experiments	best	0.987	0.977	0.978	0.964	0.958	0.939
Non-Methyl HT-SELEX, 4 experiments	median	0.974	0.959	0.946	0.923	0.868	0.84
Non-Methyl HT-SELEX, 4 experiments	best	0.985	0.974	0.975	0.96	0.955	0.935

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.994	0.968	0.961	0.64
batch 2	0.719	0.555	0.751	0.529

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

PCM	VAX2.H12INVIVO.0.SM.D.pcm
PWM	VAX2.H12INVIVO.0.SM.D.pwm
PFM	VAX2.H12INVIVO.0.SM.D.pfm
Alignment	VAX2.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	VAX2.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	VAX2.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	VAX2.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	VAX2.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	VAX2.H12INVIVO.0.SM.D_homer_format_0.001.txt VAX2.H12INVIVO.0.SM.D_homer_format_0.0005.txt VAX2.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2363.25	1939.25	2905.25	1840.25
02	1475.25	3056.25	3294.25	1222.25
03	984.0	3220.0	4165.0	679.0
04	33.0	1054.0	27.0	7934.0
05	5659.0	3319.0	58.0	12.0
06	9048.0	0.0	0.0	0.0
07	0.0	0.0	0.0	9048.0
08	0.0	0.0	0.0	9048.0
09	9048.0	0.0	0.0	0.0
10	2564.0	920.0	5459.0	105.0
11	296.0	3930.0	2209.0	2613.0
12	1487.25	1857.25	4066.25	1637.25
13	2162.25	2401.25	2160.25	2324.25

PFM

	A	C	G	T
01	0.261	0.214	0.321	0.203
02	0.163	0.338	0.364	0.135
03	0.109	0.356	0.46	0.075
04	0.004	0.116	0.003	0.877
05	0.625	0.367	0.006	0.001
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	0.283	0.102	0.603	0.012
11	0.033	0.434	0.244	0.289
12	0.164	0.205	0.449	0.181
13	0.239	0.265	0.239	0.257

PWM

	A	C	G	T
01	0.044	-0.154	0.25	-0.206
02	-0.427	0.301	0.376	-0.615
03	-0.831	0.353	0.61	-1.201
04	-4.162	-0.763	-4.348	1.254
05	0.916	0.383	-3.626	-5.066
06	1.386	-6.902	-6.902	-6.902
07	-6.902	-6.902	-6.902	1.386
08	-6.902	-6.902	-6.902	1.386
09	1.386	-6.902	-6.902	-6.902
10	0.125	-0.898	0.88	-3.05
11	-2.027	0.552	-0.024	0.144
12	-0.419	-0.197	0.586	-0.323
13	-0.045	0.06	-0.046	0.027

Standard thresholds

P-value	Threshold
0.001	2.88136
0.0005	4.986625
0.0001	7.78812