VENTX.H12RSNP.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VENTX.H12RSNP.0.SM.B
Gene (human)	VENTX (GeneCards)
Gene synonyms (human)	HPX42B, VENTX2
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nvYRATTARbvn
GC content	38.15%
Information content (bits; total / per base)	10.539 / 0.878
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	7938

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.936	0.904	0.9	0.863	0.857	0.819
Overall, 4 experiments	best	0.976	0.959	0.961	0.939	0.932	0.904
Methyl HT-SELEX, 1 experiments	median	0.976	0.959	0.961	0.939	0.932	0.904
Methyl HT-SELEX, 1 experiments	best	0.976	0.959	0.961	0.939	0.932	0.904
Non-Methyl HT-SELEX, 3 experiments	median	0.899	0.853	0.844	0.794	0.79	0.743
Non-Methyl HT-SELEX, 3 experiments	best	0.973	0.954	0.957	0.933	0.925	0.895

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.946	0.133	0.941	0.573
batch 2	0.783	0.203	0.797	0.506

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	VENTX {3.1.2.23} (TFClass)
TFClass ID	TFClass: 3.1.2.23.1
HGNC	HGNC:13639
MGI
EntrezGene (human)	GeneID:27287 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	VENTX_HUMAN
UniProt ID (mouse)
UniProt AC (human)	O95231 (TFClass)
UniProt AC (mouse)
GRECO-DB-TF	yes

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

PCM	VENTX.H12RSNP.0.SM.B.pcm
PWM	VENTX.H12RSNP.0.SM.B.pwm
PFM	VENTX.H12RSNP.0.SM.B.pfm
Alignment	VENTX.H12RSNP.0.SM.B.words.tsv
Threshold to P-value map	VENTX.H12RSNP.0.SM.B.thr
Motif in other formats
JASPAR format	VENTX.H12RSNP.0.SM.B_jaspar_format.txt
MEME format	VENTX.H12RSNP.0.SM.B_meme_format.meme
Transfac format	VENTX.H12RSNP.0.SM.B_transfac_format.txt
Homer format	VENTX.H12RSNP.0.SM.B_homer_format_0.001.txt VENTX.H12RSNP.0.SM.B_homer_format_0.0005.txt VENTX.H12RSNP.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3110.75	1365.75	1695.75	1765.75
02	1417.5	3099.5	2256.5	1164.5
03	357.0	4137.0	263.0	3181.0
04	3492.0	2066.0	2346.0	34.0
05	7932.0	2.0	4.0	0.0
06	0.0	0.0	0.0	7938.0
07	0.0	0.0	0.0	7938.0
08	7937.0	1.0	0.0	0.0
09	2999.0	98.0	4668.0	173.0
10	262.0	3707.0	2030.0	1939.0
11	2107.25	1191.25	3617.25	1022.25
12	2231.5	1834.5	1959.5	1912.5

PFM

	A	C	G	T
01	0.392	0.172	0.214	0.222
02	0.179	0.39	0.284	0.147
03	0.045	0.521	0.033	0.401
04	0.44	0.26	0.296	0.004
05	0.999	0.0	0.001	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	0.378	0.012	0.588	0.022
10	0.033	0.467	0.256	0.244
11	0.265	0.15	0.456	0.129
12	0.281	0.231	0.247	0.241

PWM

	A	C	G	T
01	0.449	-0.373	-0.157	-0.117
02	-0.336	0.445	0.128	-0.532
03	-1.71	0.734	-2.014	0.471
04	0.565	0.04	0.167	-4.004
05	1.385	-6.149	-5.762	-6.786
06	-6.786	-6.786	-6.786	1.385
07	-6.786	-6.786	-6.786	1.385
08	1.385	-6.417	-6.786	-6.786
09	0.413	-2.987	0.855	-2.428
10	-2.017	0.624	0.023	-0.023
11	0.06	-0.51	0.6	-0.662
12	0.117	-0.079	-0.013	-0.037

Standard thresholds

P-value	Threshold
0.001	4.56978
0.0005	6.072935
0.0001	7.771675