VSX2.H12INVIVO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12INVIVO.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	nvYTAATTAGChWWWWd
GC content	32.97%
Information content (bits; total / per base)	18.406 / 1.083
Data sources	HT-SELEX
Aligned words	1605

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)	0.978	0.981	0.966	0.976	0.976	0.981	5.602	5.702	355.77	421.337

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.994	0.993	0.99	0.977	0.97
Overall, 6 experiments	best	0.999	0.998	0.998	0.996	0.994	0.991
Methyl HT-SELEX, 2 experiments	median	0.99	0.983	0.984	0.975	0.967	0.955
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.998	0.996	0.994	0.991
Non-Methyl HT-SELEX, 4 experiments	median	0.997	0.994	0.993	0.99	0.977	0.97
Non-Methyl HT-SELEX, 4 experiments	best	0.997	0.996	0.994	0.991	0.987	0.981

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.917	0.253	0.917	0.586
batch 2	0.848	0.684	0.854	0.637

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.H12INVIVO.1.S.B.pcm
PWM	VSX2.H12INVIVO.1.S.B.pwm
PFM	VSX2.H12INVIVO.1.S.B.pfm
Alignment	VSX2.H12INVIVO.1.S.B.words.tsv
Threshold to P-value map	VSX2.H12INVIVO.1.S.B.thr
Motif in other formats
JASPAR format	VSX2.H12INVIVO.1.S.B_jaspar_format.txt
MEME format	VSX2.H12INVIVO.1.S.B_meme_format.meme
Transfac format	VSX2.H12INVIVO.1.S.B_transfac_format.txt
Homer format	VSX2.H12INVIVO.1.S.B_homer_format_0.001.txt VSX2.H12INVIVO.1.S.B_homer_format_0.0005.txt VSX2.H12INVIVO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	329.5	484.5	520.5	270.5
02	316.5	266.5	910.5	111.5
03	49.0	1196.0	158.0	202.0
04	0.0	13.0	0.0	1592.0
05	1604.0	1.0	0.0	0.0
06	1605.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1605.0
08	0.0	0.0	0.0	1605.0
09	1602.0	0.0	3.0	0.0
10	45.0	11.0	1547.0	2.0
11	24.0	1282.0	63.0	236.0
12	140.0	746.0	118.0	601.0
13	974.0	242.0	78.0	311.0
14	989.0	259.0	71.0	286.0
15	393.0	177.0	75.0	960.0
16	371.5	197.5	101.5	934.5
17	687.0	187.0	288.0	443.0

PFM

	A	C	G	T
01	0.205	0.302	0.324	0.169
02	0.197	0.166	0.567	0.069
03	0.031	0.745	0.098	0.126
04	0.0	0.008	0.0	0.992
05	0.999	0.001	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	0.998	0.0	0.002	0.0
10	0.028	0.007	0.964	0.001
11	0.015	0.799	0.039	0.147
12	0.087	0.465	0.074	0.374
13	0.607	0.151	0.049	0.194
14	0.616	0.161	0.044	0.178
15	0.245	0.11	0.047	0.598
16	0.231	0.123	0.063	0.582
17	0.428	0.117	0.179	0.276

PWM

	A	C	G	T
01	-0.196	0.188	0.259	-0.392
02	-0.236	-0.407	0.817	-1.269
03	-2.07	1.089	-0.925	-0.682
04	-5.387	-3.301	-5.387	1.375
05	1.382	-4.954	-5.387	-5.387
06	1.383	-5.387	-5.387	-5.387
07	-5.387	-5.387	-5.387	1.383
08	-5.387	-5.387	-5.387	1.383
09	1.381	-5.387	-4.421	-5.387
10	-2.152	-3.446	1.346	-4.652
11	-2.747	1.158	-1.827	-0.528
12	-1.044	0.618	-1.213	0.402
13	0.884	-0.503	-1.619	-0.253
14	0.899	-0.435	-1.711	-0.337
15	-0.021	-0.813	-1.657	0.87
16	-0.077	-0.704	-1.361	0.843
17	0.536	-0.758	-0.33	0.099

Standard thresholds

P-value	Threshold
0.001	-0.63839
0.0005	1.08641
0.0001	4.60411