VSX2.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12INVITRO.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	12
Consensus	vbTAATTAGChn
GC content	37.24%
Information content (bits; total / per base)	15.443 / 1.287
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9856

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)	0.989	0.993	0.982	0.99	0.984	0.988	5.837	5.926	399.569	446.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.998	0.997	0.995	0.993	0.979	0.973
Overall, 6 experiments	best	0.999	0.998	0.999	0.998	0.997	0.995
Methyl HT-SELEX, 2 experiments	median	0.992	0.986	0.988	0.98	0.97	0.96
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.999	0.998	0.997	0.995
Non-Methyl HT-SELEX, 4 experiments	median	0.998	0.997	0.995	0.993	0.979	0.973
Non-Methyl HT-SELEX, 4 experiments	best	0.998	0.997	0.996	0.994	0.992	0.988

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.959	0.383	0.95	0.642
batch 2	0.863	0.686	0.879	0.673

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.H12INVITRO.0.PSM.A.pcm
PWM	VSX2.H12INVITRO.0.PSM.A.pwm
PFM	VSX2.H12INVITRO.0.PSM.A.pfm
Alignment	VSX2.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	VSX2.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	VSX2.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	VSX2.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	VSX2.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	VSX2.H12INVITRO.0.PSM.A_homer_format_0.001.txt VSX2.H12INVITRO.0.PSM.A_homer_format_0.0005.txt VSX2.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1963.0	3249.0	3403.0	1241.0
02	827.5	5349.5	2153.5	1525.5
03	129.0	512.0	30.0	9185.0
04	9781.0	5.0	69.0	1.0
05	9856.0	0.0	0.0	0.0
06	0.0	0.0	0.0	9856.0
07	0.0	0.0	0.0	9856.0
08	9746.0	0.0	110.0	0.0
09	78.0	276.0	9500.0	2.0
10	23.0	9089.0	530.0	214.0
11	1012.75	4554.75	894.75	3393.75
12	2994.25	2439.25	1879.25	2543.25

PFM

	A	C	G	T
01	0.199	0.33	0.345	0.126
02	0.084	0.543	0.218	0.155
03	0.013	0.052	0.003	0.932
04	0.992	0.001	0.007	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	0.989	0.0	0.011	0.0
09	0.008	0.028	0.964	0.0
10	0.002	0.922	0.054	0.022
11	0.103	0.462	0.091	0.344
12	0.304	0.247	0.191	0.258

PWM

	A	C	G	T
01	-0.227	0.276	0.323	-0.685
02	-1.089	0.775	-0.135	-0.479
03	-2.933	-1.568	-4.335	1.315
04	1.378	-5.823	-3.544	-6.617
05	1.386	-6.978	-6.978	-6.978
06	-6.978	-6.978	-6.978	1.386
07	-6.978	-6.978	-6.978	1.386
08	1.374	-6.978	-3.089	-6.978
09	-3.425	-2.182	1.349	-6.352
10	-4.58	1.305	-1.533	-2.434
11	-0.888	0.614	-1.011	0.32
12	0.195	-0.01	-0.271	0.032

Standard thresholds

P-value	Threshold
0.001	0.29607
0.0005	2.18292
0.0001	5.89491