SOX10.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX10.H12RSNP.1.PSM.A
Gene (human)	SOX10 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox10
Gene synonyms (mouse)	Sox-10, Sox21
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	11
Consensus	nSCATTGTYhn
GC content	38.23%
Information content (bits; total / per base)	12.666 / 1.151
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9325

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)	0.783	0.811	0.628	0.644	0.776	0.81	2.112	2.226	102.695	124.854
Mouse	1 (6)	0.699	0.754	0.534	0.578	0.698	0.741	1.735	1.878	50.446	96.319

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.973	0.953	0.904	0.906	0.721	0.755
Overall, 5 experiments	best	0.993	0.989	0.983	0.973	0.923	0.917
Methyl HT-SELEX, 2 experiments	median	0.992	0.986	0.943	0.939	0.822	0.836
Methyl HT-SELEX, 2 experiments	best	0.993	0.989	0.983	0.973	0.923	0.917
Non-Methyl HT-SELEX, 3 experiments	median	0.797	0.789	0.659	0.665	0.594	0.602
Non-Methyl HT-SELEX, 3 experiments	best	0.973	0.953	0.936	0.914	0.783	0.79

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.666	0.362	0.601	0.402

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.1.PSM.A.pcm
PWM	SOX10.H12RSNP.1.PSM.A.pwm
PFM	SOX10.H12RSNP.1.PSM.A.pfm
Alignment	SOX10.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	SOX10.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	SOX10.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	SOX10.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	SOX10.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	SOX10.H12RSNP.1.PSM.A_homer_format_0.001.txt SOX10.H12RSNP.1.PSM.A_homer_format_0.0005.txt SOX10.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1841.5	2564.5	2250.5	2668.5
02	169.0	5554.0	1857.0	1745.0
03	71.0	6412.0	7.0	2835.0
04	8985.0	0.0	0.0	340.0
05	0.0	0.0	0.0	9325.0
06	0.0	0.0	0.0	9325.0
07	0.0	0.0	9325.0	0.0
08	0.0	0.0	0.0	9325.0
09	431.0	1574.0	193.0	7127.0
10	1559.25	4657.25	631.25	2477.25
11	1814.0	2464.0	1725.0	3322.0

PFM

	A	C	G	T
01	0.197	0.275	0.241	0.286
02	0.018	0.596	0.199	0.187
03	0.008	0.688	0.001	0.304
04	0.964	0.0	0.0	0.036
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.046	0.169	0.021	0.764
10	0.167	0.499	0.068	0.266
11	0.195	0.264	0.185	0.356

PWM

	A	C	G	T
01	-0.236	0.095	-0.035	0.135
02	-2.612	0.868	-0.227	-0.289
03	-3.461	1.011	-5.527	0.195
04	1.348	-6.929	-6.929	-1.919
05	-6.929	-6.929	-6.929	1.386
06	-6.929	-6.929	-6.929	1.386
07	-6.929	-6.929	1.386	-6.929
08	-6.929	-6.929	-6.929	1.386
09	-1.684	-0.392	-2.481	1.117
10	-0.402	0.692	-1.304	0.061
11	-0.251	0.055	-0.301	0.354

Standard thresholds

P-value	Threshold
0.001	1.89235
0.0005	4.310355
0.0001	7.601345