VSX2.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12RSNP.1.S.B
Gene (human)	VSX2 (GeneCards)
Gene synonyms (human)	CHX10, HOX10
Gene (mouse)	Vsx2
Gene synonyms (mouse)	Chx10
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	nvYTAATTAGYhhhhhd
GC content	32.15%
Information content (bits; total / per base)	16.856 / 0.992
Data sources	HT-SELEX
Aligned words	2345

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	1 (7)	0.975	0.981	0.961	0.974	0.973	0.978	5.521	5.621	355.886	420.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.994	0.993	0.99	0.978	0.972
Overall, 6 experiments	best	0.998	0.997	0.997	0.996	0.994	0.991
Methyl HT-SELEX, 2 experiments	median	0.99	0.983	0.985	0.976	0.97	0.958
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.997	0.996	0.994	0.991
Non-Methyl HT-SELEX, 4 experiments	median	0.997	0.994	0.993	0.99	0.978	0.972
Non-Methyl HT-SELEX, 4 experiments	best	0.997	0.996	0.994	0.99	0.987	0.981

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.928	0.285	0.922	0.599
batch 2	0.857	0.702	0.858	0.646

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: 3.1.3.28.2
HGNC	HGNC:1975
MGI	MGI:88401
EntrezGene (human)	GeneID:338917 (SSTAR profile)
EntrezGene (mouse)	GeneID:12677 (SSTAR profile)
UniProt ID (human)	VSX2_HUMAN
UniProt ID (mouse)	VSX2_MOUSE
UniProt AC (human)	P58304 (TFClass)
UniProt AC (mouse)	Q61412 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	VSX2.H12RSNP.1.S.B.pcm
PWM	VSX2.H12RSNP.1.S.B.pwm
PFM	VSX2.H12RSNP.1.S.B.pfm
Alignment	VSX2.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	VSX2.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	VSX2.H12RSNP.1.S.B_jaspar_format.txt
MEME format	VSX2.H12RSNP.1.S.B_meme_format.meme
Transfac format	VSX2.H12RSNP.1.S.B_transfac_format.txt
Homer format	VSX2.H12RSNP.1.S.B_homer_format_0.001.txt VSX2.H12RSNP.1.S.B_homer_format_0.0005.txt VSX2.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	534.25	684.25	726.25	400.25
02	545.5	442.5	1165.5	191.5
03	53.0	1582.0	300.0	410.0
04	2.0	46.0	0.0	2297.0
05	2345.0	0.0	0.0	0.0
06	2345.0	0.0	0.0	0.0
07	0.0	0.0	0.0	2345.0
08	0.0	0.0	0.0	2345.0
09	2321.0	0.0	24.0	0.0
10	144.0	63.0	2134.0	4.0
11	49.0	1693.0	156.0	447.0
12	306.0	973.0	271.0	795.0
13	1226.0	388.0	178.0	553.0
14	1277.0	372.0	156.0	540.0
15	687.0	292.0	125.0	1241.0
16	692.0	269.0	143.0	1241.0
17	933.5	263.5	369.5	778.5

PFM

	A	C	G	T
01	0.228	0.292	0.31	0.171
02	0.233	0.189	0.497	0.082
03	0.023	0.675	0.128	0.175
04	0.001	0.02	0.0	0.98
05	1.0	0.0	0.0	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	0.99	0.0	0.01	0.0
10	0.061	0.027	0.91	0.002
11	0.021	0.722	0.067	0.191
12	0.13	0.415	0.116	0.339
13	0.523	0.165	0.076	0.236
14	0.545	0.159	0.067	0.23
15	0.293	0.125	0.053	0.529
16	0.295	0.115	0.061	0.529
17	0.398	0.112	0.158	0.332

PWM

	A	C	G	T
01	-0.093	0.154	0.214	-0.38
02	-0.072	-0.28	0.686	-1.112
03	-2.371	0.991	-0.667	-0.356
04	-5.006	-2.507	-5.714	1.363
05	1.384	-5.714	-5.714	-5.714
06	1.384	-5.714	-5.714	-5.714
07	-5.714	-5.714	-5.714	1.384
08	-5.714	-5.714	-5.714	1.384
09	1.374	-5.714	-3.121	-5.714
10	-1.394	-2.204	1.29	-4.595
11	-2.446	1.058	-1.315	-0.27
12	-0.647	0.505	-0.768	0.304
13	0.736	-0.411	-1.184	-0.058
14	0.777	-0.453	-1.315	-0.082
15	0.158	-0.694	-1.533	0.748
16	0.165	-0.775	-1.401	0.748
17	0.464	-0.796	-0.46	0.283

Standard thresholds

P-value	Threshold
0.001	0.25441
0.0005	1.91141
0.0001	5.38046