VSX2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12INVIVO.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	11
Consensus	hTAATTAGCYd
GC content	28.62%
Information content (bits; total / per base)	16.561 / 1.506
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1015

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)	0.99	0.995	0.986	0.992	0.988	0.991	6.149	6.255	388.553	447.252

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.995	0.993	0.991	0.971	0.965
Overall, 6 experiments	best	0.999	0.997	0.999	0.997	0.996	0.994
Methyl HT-SELEX, 2 experiments	median	0.991	0.984	0.987	0.978	0.968	0.957
Methyl HT-SELEX, 2 experiments	best	0.999	0.997	0.999	0.997	0.996	0.994
Non-Methyl HT-SELEX, 4 experiments	median	0.997	0.995	0.993	0.991	0.971	0.965
Non-Methyl HT-SELEX, 4 experiments	best	0.998	0.996	0.996	0.992	0.991	0.986

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.909	0.225	0.936	0.574
batch 2	0.849	0.652	0.858	0.64

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.0.PSM.A.pcm
PWM	VSX2.H12INVIVO.0.PSM.A.pwm
PFM	VSX2.H12INVIVO.0.PSM.A.pfm
Alignment	VSX2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	VSX2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	VSX2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	VSX2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	VSX2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	VSX2.H12INVIVO.0.PSM.A_homer_format_0.001.txt VSX2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt VSX2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	133.0	378.0	79.0	425.0
02	15.0	7.0	2.0	991.0
03	995.0	6.0	11.0	3.0
04	1014.0	1.0	0.0	0.0
05	0.0	0.0	5.0	1010.0
06	0.0	1.0	2.0	1012.0
07	1004.0	1.0	10.0	0.0
08	8.0	8.0	998.0	1.0
09	1.0	1007.0	2.0	5.0
10	24.0	364.0	3.0	624.0
11	244.0	145.0	165.0	461.0

PFM

	A	C	G	T
01	0.131	0.372	0.078	0.419
02	0.015	0.007	0.002	0.976
03	0.98	0.006	0.011	0.003
04	0.999	0.001	0.0	0.0
05	0.0	0.0	0.005	0.995
06	0.0	0.001	0.002	0.997
07	0.989	0.001	0.01	0.0
08	0.008	0.008	0.983	0.001
09	0.001	0.992	0.002	0.005
10	0.024	0.359	0.003	0.615
11	0.24	0.143	0.163	0.454

PWM

	A	C	G	T
01	-0.64	0.396	-1.152	0.513
02	-2.726	-3.376	-4.227	1.357
03	1.361	-3.498	-2.999	-3.989
04	1.38	-4.539	-4.995	-4.995
05	-4.995	-4.995	-3.636	1.376
06	-4.995	-4.539	-4.227	1.378
07	1.37	-4.539	-3.081	-4.995
08	-3.268	-3.268	1.364	-4.539
09	-4.539	1.373	-4.227	-3.636
10	-2.295	0.359	-3.989	0.896
11	-0.039	-0.555	-0.427	0.594

Standard thresholds

P-value	Threshold
0.001	0.841975
0.0005	1.962295
0.0001	5.86964