VSX2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12RSNP.0.PSM.A
Gene (human)	VSX2 (GeneCards)
Gene synonyms (human)	CHX10, HOX10
Gene (mouse)	Vsx2
Gene synonyms (mouse)	Chx10
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	10
Consensus	nYAATTARbn
GC content	31.47%
Information content (bits; total / per base)	11.487 / 1.149
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9679

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)	0.987	0.991	0.98	0.987	0.98	0.984	5.584	5.705	387.328	441.215

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.996	0.994	0.992	0.979	0.971
Overall, 6 experiments	best	0.999	0.998	0.998	0.997	0.994	0.992
Methyl HT-SELEX, 2 experiments	median	0.992	0.986	0.988	0.98	0.977	0.966
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.997	0.994	0.992
Non-Methyl HT-SELEX, 4 experiments	median	0.997	0.996	0.994	0.992	0.979	0.971
Non-Methyl HT-SELEX, 4 experiments	best	0.998	0.997	0.995	0.992	0.988	0.982

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.969	0.498	0.959	0.642
batch 2	0.881	0.735	0.892	0.689

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.0.PSM.A.pcm
PWM	VSX2.H12RSNP.0.PSM.A.pwm
PFM	VSX2.H12RSNP.0.PSM.A.pfm
Alignment	VSX2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	VSX2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	VSX2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	VSX2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	VSX2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	VSX2.H12RSNP.0.PSM.A_homer_format_0.001.txt VSX2.H12RSNP.0.PSM.A_homer_format_0.0005.txt VSX2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1372.75	3088.75	2729.75	2487.75
02	363.75	3358.75	244.75	5711.75
03	9227.0	213.0	227.0	12.0
04	9672.0	4.0	3.0	0.0
05	0.0	0.0	0.0	9679.0
06	0.0	0.0	0.0	9679.0
07	9669.0	0.0	10.0	0.0
08	1658.0	1254.0	6570.0	197.0
09	488.25	5105.25	2168.25	1917.25
10	1595.75	2651.75	2831.75	2599.75

PFM

	A	C	G	T
01	0.142	0.319	0.282	0.257
02	0.038	0.347	0.025	0.59
03	0.953	0.022	0.023	0.001
04	0.999	0.0	0.0	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.999	0.0	0.001	0.0
08	0.171	0.13	0.679	0.02
09	0.05	0.527	0.224	0.198
10	0.165	0.274	0.293	0.269

PWM

	A	C	G	T
01	-0.566	0.244	0.12	0.028
02	-1.89	0.328	-2.283	0.858
03	1.338	-2.42	-2.357	-5.132
04	1.385	-5.953	-6.126	-6.962
05	-6.962	-6.962	-6.962	1.386
06	-6.962	-6.962	-6.962	1.386
07	1.385	-6.962	-5.283	-6.962
08	-0.378	-0.656	0.998	-2.498
09	-1.597	0.746	-0.11	-0.233
10	-0.416	0.091	0.157	0.072

Standard thresholds

P-value	Threshold
0.001	3.758455
0.0005	5.30135
0.0001	7.807765