SOX10.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX10.H12INVIVO.0.PSM.A
Gene (human)	SOX10 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox10
Gene synonyms (mouse)	Sox-10, Sox21
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	17
Consensus	vARdRvnnbCWTTGTbb
GC content	40.5%
Information content (bits; total / per base)	12.613 / 0.742
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)	0.918	0.942	0.861	0.894	0.905	0.929	3.793	3.992	228.292	266.143
Mouse	1 (6)	0.825	0.904	0.779	0.86	0.828	0.89	3.273	3.783	123.46	209.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.987	0.983	0.856	0.861	0.672	0.716
Overall, 5 experiments	best	1.0	0.999	0.998	0.998	0.927	0.935
Methyl HT-SELEX, 2 experiments	median	0.993	0.991	0.927	0.929	0.8	0.826
Methyl HT-SELEX, 2 experiments	best	1.0	0.999	0.998	0.998	0.927	0.935
Non-Methyl HT-SELEX, 3 experiments	median	0.763	0.763	0.608	0.634	0.553	0.574
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.997	0.957	0.956	0.762	0.797

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.625	0.341	0.483	0.281

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.0.PSM.A.pcm
PWM	SOX10.H12INVIVO.0.PSM.A.pwm
PFM	SOX10.H12INVIVO.0.PSM.A.pfm
Alignment	SOX10.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SOX10.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX10.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SOX10.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SOX10.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SOX10.H12INVIVO.0.PSM.A_homer_format_0.001.txt SOX10.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SOX10.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	341.0	392.0	179.0	88.0
02	903.0	68.0	12.0	17.0
03	757.0	46.0	99.0	98.0
04	402.0	30.0	224.0	344.0
05	268.0	83.0	582.0	67.0
06	211.0	247.0	469.0	73.0
07	311.0	264.0	263.0	162.0
08	260.0	235.0	240.0	265.0
09	26.0	318.0	355.0	301.0
10	46.0	802.0	24.0	128.0
11	447.0	30.0	2.0	521.0
12	3.0	70.0	33.0	894.0
13	2.0	27.0	3.0	968.0
14	65.0	20.0	913.0	2.0
15	39.0	0.0	6.0	955.0
16	100.0	176.0	179.0	545.0
17	82.0	377.0	117.0	424.0

PFM

	A	C	G	T
01	0.341	0.392	0.179	0.088
02	0.903	0.068	0.012	0.017
03	0.757	0.046	0.099	0.098
04	0.402	0.03	0.224	0.344
05	0.268	0.083	0.582	0.067
06	0.211	0.247	0.469	0.073
07	0.311	0.264	0.263	0.162
08	0.26	0.235	0.24	0.265
09	0.026	0.318	0.355	0.301
10	0.046	0.802	0.024	0.128
11	0.447	0.03	0.002	0.521
12	0.003	0.07	0.033	0.894
13	0.002	0.027	0.003	0.968
14	0.065	0.02	0.913	0.002
15	0.039	0.0	0.006	0.955
16	0.1	0.176	0.179	0.545
17	0.082	0.377	0.117	0.424

PWM

	A	C	G	T
01	0.309	0.447	-0.331	-1.032
02	1.279	-1.284	-2.909	-2.598
03	1.103	-1.663	-0.916	-0.926
04	0.472	-2.071	-0.109	0.317
05	0.069	-1.089	0.841	-1.298
06	-0.168	-0.012	0.626	-1.215
07	0.217	0.054	0.05	-0.43
08	0.039	-0.061	-0.041	0.058
09	-2.206	0.239	0.349	0.184
10	-1.663	1.161	-2.281	-0.663
11	0.578	-2.071	-4.213	0.731
12	-3.975	-1.255	-1.981	1.269
13	-4.213	-2.171	-3.975	1.349
14	-1.328	-2.45	1.29	-4.213
15	-1.821	-4.982	-3.484	1.335
16	-0.906	-0.348	-0.331	0.776
17	-1.101	0.408	-0.752	0.525

Standard thresholds

P-value	Threshold
0.001	3.97931
0.0005	4.99881
0.0001	7.09256