SOX10.H12INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX10.H12INVITRO.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	nbYATTGTThn
GC content	40.25%
Information content (bits; total / per base)	11.488 / 1.044
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	514

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)	0.782	0.797	0.627	0.64	0.732	0.763	1.975	2.075	96.228	115.509
Mouse	1 (6)	0.701	0.754	0.541	0.587	0.652	0.693	1.593	1.739	45.386	96.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.973	0.953	0.916	0.909	0.73	0.763
Overall, 5 experiments	best	0.992	0.988	0.981	0.971	0.922	0.914
Methyl HT-SELEX, 2 experiments	median	0.991	0.985	0.949	0.942	0.826	0.838
Methyl HT-SELEX, 2 experiments	best	0.992	0.988	0.981	0.971	0.922	0.914
Non-Methyl HT-SELEX, 3 experiments	median	0.817	0.81	0.676	0.68	0.605	0.613
Non-Methyl HT-SELEX, 3 experiments	best	0.973	0.953	0.932	0.909	0.793	0.794

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.68	0.352	0.572	0.377

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.H12INVITRO.1.PSM.A.pcm
PWM	SOX10.H12INVITRO.1.PSM.A.pwm
PFM	SOX10.H12INVITRO.1.PSM.A.pfm
Alignment	SOX10.H12INVITRO.1.PSM.A.words.tsv
Threshold to P-value map	SOX10.H12INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	SOX10.H12INVITRO.1.PSM.A_jaspar_format.txt
MEME format	SOX10.H12INVITRO.1.PSM.A_meme_format.meme
Transfac format	SOX10.H12INVITRO.1.PSM.A_transfac_format.txt
Homer format	SOX10.H12INVITRO.1.PSM.A_homer_format_0.001.txt SOX10.H12INVITRO.1.PSM.A_homer_format_0.0005.txt SOX10.H12INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	104.75	150.75	151.75	106.75
02	41.25	271.25	123.25	78.25
03	16.0	361.0	25.0	112.0
04	466.0	27.0	10.0	11.0
05	0.0	0.0	0.0	514.0
06	0.0	1.0	0.0	513.0
07	0.0	5.0	509.0	0.0
08	10.0	12.0	0.0	492.0
09	28.0	24.0	43.0	419.0
10	82.5	272.5	60.5	98.5
11	104.75	116.75	111.75	180.75

PFM

	A	C	G	T
01	0.204	0.293	0.295	0.208
02	0.08	0.528	0.24	0.152
03	0.031	0.702	0.049	0.218
04	0.907	0.053	0.019	0.021
05	0.0	0.0	0.0	1.0
06	0.0	0.002	0.0	0.998
07	0.0	0.01	0.99	0.0
08	0.019	0.023	0.0	0.957
09	0.054	0.047	0.084	0.815
10	0.161	0.53	0.118	0.192
11	0.204	0.227	0.217	0.352

PWM

	A	C	G	T
01	-0.202	0.158	0.164	-0.183
02	-1.111	0.741	-0.041	-0.488
03	-2.002	1.025	-1.589	-0.136
04	1.28	-1.516	-2.42	-2.337
05	-4.423	-4.423	-4.423	1.377
06	-4.423	-3.928	-4.423	1.375
07	-4.423	-2.987	1.368	-4.423
08	-2.42	-2.261	-4.423	1.334
09	-1.482	-1.627	-1.071	1.174
10	-0.436	0.745	-0.74	-0.262
11	-0.202	-0.095	-0.138	0.338

Standard thresholds

P-value	Threshold
0.001	4.333755
0.0005	5.41158
0.0001	7.441105