VSX1.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX1.H12INVITRO.1.SM.B
Gene (human)	VSX1 (GeneCards)
Gene synonyms (human)	RINX
Gene (mouse)	Vsx1
Gene synonyms (mouse)	Rinx
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	nnvSTAATTAGCYhvhh
GC content	38.0%
Information content (bits; total / per base)	16.577 / 0.975
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	749

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 10 experiments	median	0.996	0.993	0.986	0.98	0.956	0.941
Overall, 10 experiments	best	0.998	0.997	0.995	0.993	0.985	0.98
Methyl HT-SELEX, 2 experiments	median	0.985	0.975	0.978	0.964	0.959	0.942
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	0.993	0.986	0.98	0.956	0.941
Non-Methyl HT-SELEX, 8 experiments	best	0.997	0.996	0.993	0.99	0.979	0.972

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.892	0.077	0.871	0.497
batch 2	0.883	0.736	0.749	0.523

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.H12INVITRO.1.SM.B.pcm
PWM	VSX1.H12INVITRO.1.SM.B.pwm
PFM	VSX1.H12INVITRO.1.SM.B.pfm
Alignment	VSX1.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	VSX1.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	VSX1.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	VSX1.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	VSX1.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	VSX1.H12INVITRO.1.SM.B_homer_format_0.001.txt VSX1.H12INVITRO.1.SM.B_homer_format_0.0005.txt VSX1.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	158.75	195.75	172.75	221.75
02	132.5	284.5	130.5	201.5
03	138.0	181.0	383.0	47.0
04	31.0	506.0	107.0	105.0
05	0.0	41.0	1.0	707.0
06	749.0	0.0	0.0	0.0
07	749.0	0.0	0.0	0.0
08	0.0	0.0	0.0	749.0
09	0.0	0.0	0.0	749.0
10	744.0	0.0	5.0	0.0
11	30.0	42.0	672.0	5.0
12	3.0	634.0	77.0	35.0
13	29.0	322.0	73.0	325.0
14	314.0	213.0	48.0	174.0
15	396.0	179.0	97.0	77.0
16	218.0	164.0	67.0	300.0
17	141.75	130.75	111.75	364.75

PFM

	A	C	G	T
01	0.212	0.261	0.231	0.296
02	0.177	0.38	0.174	0.269
03	0.184	0.242	0.511	0.063
04	0.041	0.676	0.143	0.14
05	0.0	0.055	0.001	0.944
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.0	1.0
10	0.993	0.0	0.007	0.0
11	0.04	0.056	0.897	0.007
12	0.004	0.846	0.103	0.047
13	0.039	0.43	0.097	0.434
14	0.419	0.284	0.064	0.232
15	0.529	0.239	0.13	0.103
16	0.291	0.219	0.089	0.401
17	0.189	0.175	0.149	0.487

PWM

	A	C	G	T
01	-0.164	0.044	-0.08	0.168
02	-0.342	0.415	-0.357	0.073
03	-0.302	-0.034	0.711	-1.356
04	-1.755	0.989	-0.553	-0.572
05	-4.738	-1.488	-4.265	1.322
06	1.38	-4.738	-4.738	-4.738
07	1.38	-4.738	-4.738	-4.738
08	-4.738	-4.738	-4.738	1.38
09	-4.738	-4.738	-4.738	1.38
10	1.373	-4.738	-3.346	-4.738
11	-1.786	-1.465	1.271	-3.346
12	-3.703	1.213	-0.876	-1.64
13	-1.818	0.538	-0.928	0.548
14	0.513	0.128	-1.336	-0.073
15	0.744	-0.045	-0.65	-0.876
16	0.151	-0.131	-1.012	0.468
17	-0.276	-0.355	-0.51	0.662

Standard thresholds

P-value	Threshold
0.001	1.28326
0.0005	2.76736
0.0001	5.84331