VSX2.H12INVITRO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	VSX2.H12INVITRO.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	nvYTAATTAGCYWWWWd
GC content	33.18%
Information content (bits; total / per base)	18.984 / 1.117
Data sources	HT-SELEX
Aligned words	1477

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	0.98	0.964	0.975	0.975	0.981	5.627	5.726	357.409	422.745

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.997	0.995	0.994	0.991	0.977	0.971
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	0.966	0.954
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	0.995	0.994	0.991	0.977	0.971
Non-Methyl HT-SELEX, 4 experiments	best	0.998	0.996	0.995	0.991	0.987	0.981

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.917	0.24	0.916	0.587
batch 2	0.835	0.666	0.851	0.632

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.1.S.B.pcm
PWM	VSX2.H12INVITRO.1.S.B.pwm
PFM	VSX2.H12INVITRO.1.S.B.pfm
Alignment	VSX2.H12INVITRO.1.S.B.words.tsv
Threshold to P-value map	VSX2.H12INVITRO.1.S.B.thr
Motif in other formats
JASPAR format	VSX2.H12INVITRO.1.S.B_jaspar_format.txt
MEME format	VSX2.H12INVITRO.1.S.B_meme_format.meme
Transfac format	VSX2.H12INVITRO.1.S.B_transfac_format.txt
Homer format	VSX2.H12INVITRO.1.S.B_homer_format_0.001.txt VSX2.H12INVITRO.1.S.B_homer_format_0.0005.txt VSX2.H12INVITRO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	302.0	457.0	460.0	258.0
02	319.75	247.75	803.75	105.75
03	22.0	1150.0	135.0	170.0
04	0.0	7.0	0.0	1470.0
05	1477.0	0.0	0.0	0.0
06	1477.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1477.0
08	0.0	0.0	0.0	1477.0
09	1470.0	0.0	7.0	0.0
10	32.0	14.0	1431.0	0.0
11	12.0	1261.0	40.0	164.0
12	103.0	722.0	90.0	562.0
13	914.0	211.0	66.0	286.0
14	963.0	222.0	67.0	225.0
15	341.0	175.0	60.0	901.0
16	310.0	173.0	90.0	904.0
17	654.0	182.0	260.0	381.0

PFM

	A	C	G	T
01	0.204	0.309	0.311	0.175
02	0.216	0.168	0.544	0.072
03	0.015	0.779	0.091	0.115
04	0.0	0.005	0.0	0.995
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	0.995	0.0	0.005	0.0
10	0.022	0.009	0.969	0.0
11	0.008	0.854	0.027	0.111
12	0.07	0.489	0.061	0.381
13	0.619	0.143	0.045	0.194
14	0.652	0.15	0.045	0.152
15	0.231	0.118	0.041	0.61
16	0.21	0.117	0.061	0.612
17	0.443	0.123	0.176	0.258

PWM

	A	C	G	T
01	-0.2	0.212	0.219	-0.356
02	-0.143	-0.397	0.775	-1.238
03	-2.746	1.133	-0.998	-0.77
04	-5.315	-3.739	-5.315	1.378
05	1.383	-5.315	-5.315	-5.315
06	1.383	-5.315	-5.315	-5.315
07	-5.315	-5.315	-5.315	1.383
08	-5.315	-5.315	-5.315	1.383
09	1.378	-5.315	-3.739	-5.315
10	-2.395	-3.155	1.351	-5.315
11	-3.29	1.225	-2.183	-0.805
12	-1.264	0.668	-1.397	0.418
13	0.903	-0.556	-1.699	-0.254
14	0.956	-0.506	-1.685	-0.492
15	-0.079	-0.741	-1.792	0.889
16	-0.174	-0.753	-1.397	0.892
17	0.569	-0.702	-0.349	0.031

Standard thresholds

P-value	Threshold
0.001	-0.99864
0.0005	0.73191
0.0001	4.32186