SOX10.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX10.H12INVIVO.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	12
Consensus	vnbnCTTTGTKb
GC content	43.97%
Information content (bits; total / per base)	11.328 / 0.944
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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)	0.817	0.853	0.684	0.723	0.807	0.837	2.372	2.479	134.737	166.569
Mouse	1 (6)	0.736	0.796	0.606	0.648	0.763	0.809	2.12	2.354	70.869	127.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.958	0.929	0.866	0.851	0.694	0.72
Overall, 5 experiments	best	0.981	0.966	0.971	0.953	0.9	0.886
Methyl HT-SELEX, 2 experiments	median	0.974	0.956	0.918	0.902	0.797	0.803
Methyl HT-SELEX, 2 experiments	best	0.981	0.966	0.971	0.953	0.9	0.886
Non-Methyl HT-SELEX, 3 experiments	median	0.734	0.708	0.629	0.622	0.573	0.576
Non-Methyl HT-SELEX, 3 experiments	best	0.958	0.929	0.897	0.868	0.76	0.758

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.54	0.244	0.487	0.311

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.H12INVIVO.1.PSM.A.pcm
PWM	SOX10.H12INVIVO.1.PSM.A.pwm
PFM	SOX10.H12INVIVO.1.PSM.A.pfm
Alignment	SOX10.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	SOX10.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	SOX10.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	SOX10.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	SOX10.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	SOX10.H12INVIVO.1.PSM.A_homer_format_0.001.txt SOX10.H12INVIVO.1.PSM.A_homer_format_0.0005.txt SOX10.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	278.0	311.0	304.0	107.0
02	202.0	261.0	227.0	310.0
03	124.0	272.0	247.0	357.0
04	9.0	445.0	273.0	273.0
05	10.0	965.0	1.0	24.0
06	286.0	17.0	1.0	696.0
07	5.0	60.0	29.0	906.0
08	1.0	0.0	0.0	999.0
09	6.0	28.0	964.0	2.0
10	2.0	3.0	2.0	993.0
11	26.0	177.0	229.0	568.0
12	56.0	365.0	96.0	483.0

PFM

	A	C	G	T
01	0.278	0.311	0.304	0.107
02	0.202	0.261	0.227	0.31
03	0.124	0.272	0.247	0.357
04	0.009	0.445	0.273	0.273
05	0.01	0.965	0.001	0.024
06	0.286	0.017	0.001	0.696
07	0.005	0.06	0.029	0.906
08	0.001	0.0	0.0	0.999
09	0.006	0.028	0.964	0.002
10	0.002	0.003	0.002	0.993
11	0.026	0.177	0.229	0.568
12	0.056	0.365	0.096	0.483

PWM

	A	C	G	T
01	0.105	0.217	0.194	-0.84
02	-0.212	0.043	-0.096	0.214
03	-0.694	0.084	-0.012	0.354
04	-3.156	0.574	0.087	0.087
05	-3.066	1.346	-4.525	-2.281
06	0.134	-2.598	-4.525	1.019
07	-3.622	-1.406	-2.103	1.283
08	-4.525	-4.982	-4.982	1.38
09	-3.484	-2.136	1.345	-4.213
10	-4.213	-3.975	-4.213	1.374
11	-2.206	-0.342	-0.087	0.817
12	-1.473	0.376	-0.946	0.655

Standard thresholds

P-value	Threshold
0.001	4.200295
0.0005	5.275985
0.0001	7.676155