SOX10.H12RSNP.2.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX10.H12RSNP.2.S.C
Gene (human)	SOX10 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox10
Gene synonyms (mouse)	Sox-10, Sox21
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	13
Consensus	dbTGTTCGbdddn
GC content	51.27%
Information content (bits; total / per base)	10.481 / 0.806
Data sources	HT-SELEX
Aligned words	8710

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
Human	1 (6)	0.648	0.664	0.466	0.47	0.564	0.583	1.211	1.252	17.387	25.252
Mouse	1 (6)	0.58	0.607	0.406	0.428	0.562	0.579	1.214	1.257	10.14	14.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.847	0.8	0.751	0.724	0.653	0.654
Overall, 5 experiments	best	0.883	0.854	0.8	0.745	0.734	0.692
Methyl HT-SELEX, 2 experiments	median	0.819	0.766	0.755	0.707	0.691	0.657
Methyl HT-SELEX, 2 experiments	best	0.854	0.8	0.8	0.745	0.734	0.692
Non-Methyl HT-SELEX, 3 experiments	median	0.847	0.801	0.751	0.724	0.653	0.654
Non-Methyl HT-SELEX, 3 experiments	best	0.883	0.854	0.765	0.736	0.685	0.661

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.575	0.229	0.135	0.061

TF superclass	Other all-alpha-helical DNA-binding domains {4} (TFClass)
TF class	High-mobility group (HMG) domain factors {4.1} (TFClass)
TF family	SOX-related {4.1.1} (TFClass)
TF subfamily	Group E {4.1.1.5} (TFClass)
TFClass ID	TFClass: 4.1.1.5.3
HGNC	HGNC:11190
MGI	MGI:98358
EntrezGene (human)	GeneID:6663 (SSTAR profile)
EntrezGene (mouse)	GeneID:20665 (SSTAR profile)
UniProt ID (human)	SOX10_HUMAN
UniProt ID (mouse)	SOX10_MOUSE
UniProt AC (human)	P56693 (TFClass)
UniProt AC (mouse)	Q04888 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 1 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	SOX10.H12RSNP.2.S.C.pcm
PWM	SOX10.H12RSNP.2.S.C.pwm
PFM	SOX10.H12RSNP.2.S.C.pfm
Alignment	SOX10.H12RSNP.2.S.C.words.tsv
Threshold to P-value map	SOX10.H12RSNP.2.S.C.thr
Motif in other formats
JASPAR format	SOX10.H12RSNP.2.S.C_jaspar_format.txt
MEME format	SOX10.H12RSNP.2.S.C_meme_format.meme
Transfac format	SOX10.H12RSNP.2.S.C_transfac_format.txt
Homer format	SOX10.H12RSNP.2.S.C_homer_format_0.001.txt SOX10.H12RSNP.2.S.C_homer_format_0.0005.txt SOX10.H12RSNP.2.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	4127.75	879.75	2179.75	1522.75
02	849.0	1544.0	2012.0	4305.0
03	214.0	280.0	400.0	7816.0
04	179.0	71.0	8440.0	20.0
05	5.0	2.0	352.0	8351.0
06	98.0	1.0	321.0	8290.0
07	547.0	7577.0	338.0	248.0
08	598.0	531.0	7230.0	351.0
09	743.0	1424.0	5070.0	1473.0
10	976.0	881.0	3092.0	3761.0
11	1256.0	1031.0	4456.0	1967.0
12	1359.25	1229.25	4004.25	2117.25
13	1604.75	1433.75	3277.75	2393.75

PFM

	A	C	G	T
01	0.474	0.101	0.25	0.175
02	0.097	0.177	0.231	0.494
03	0.025	0.032	0.046	0.897
04	0.021	0.008	0.969	0.002
05	0.001	0.0	0.04	0.959
06	0.011	0.0	0.037	0.952
07	0.063	0.87	0.039	0.028
08	0.069	0.061	0.83	0.04
09	0.085	0.163	0.582	0.169
10	0.112	0.101	0.355	0.432
11	0.144	0.118	0.512	0.226
12	0.156	0.141	0.46	0.243
13	0.184	0.165	0.376	0.275

PWM

	A	C	G	T
01	0.639	-0.905	0.001	-0.357
02	-0.94	-0.343	-0.079	0.681
03	-2.31	-2.044	-1.69	1.277
04	-2.487	-3.393	1.354	-4.584
05	-5.703	-6.236	-1.817	1.343
06	-3.079	-6.503	-1.908	1.336
07	-1.378	1.246	-1.857	-2.164
08	-1.29	-1.408	1.199	-1.82
09	-1.073	-0.424	0.845	-0.39
10	-0.801	-0.903	0.35	0.546
11	-0.549	-0.746	0.716	-0.102
12	-0.471	-0.571	0.609	-0.028
13	-0.305	-0.417	0.409	0.095

Standard thresholds

P-value	Threshold
0.001	4.61441
0.0005	5.50006
0.0001	7.31368