SOX3.H12INVIVO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H12INVIVO.0.PM.A
Gene (human)	SOX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox3
Gene synonyms (mouse)	Sox-3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	bYYWTTGTYhbb
GC content	44.54%
Information content (bits; total / per base)	11.133 / 0.928
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	1016

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 (7)	0.793	0.804	0.653	0.659	0.794	0.809	2.207	2.323	23.796	79.444
Mouse	3 (11)	0.841	0.86	0.72	0.773	0.853	0.864	2.77	2.935	108.886	187.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.951	0.917	0.934	0.898	0.88	0.849
Overall, 2 experiments	best	0.975	0.954	0.966	0.943	0.934	0.909
Methyl HT-SELEX, 1 experiments	median	0.975	0.954	0.966	0.943	0.934	0.909
Methyl HT-SELEX, 1 experiments	best	0.975	0.954	0.966	0.943	0.934	0.909
Non-Methyl HT-SELEX, 1 experiments	median	0.927	0.88	0.902	0.853	0.826	0.789
Non-Methyl HT-SELEX, 1 experiments	best	0.927	0.88	0.902	0.853	0.826	0.789

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.587	0.273	0.416	0.265

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 B {4.1.1.2} (TFClass)
TFClass ID	TFClass: 4.1.1.2.3
HGNC	HGNC:11199
MGI	MGI:98365
EntrezGene (human)	GeneID:6658 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	SOX3_HUMAN
UniProt ID (mouse)	SOX3_MOUSE
UniProt AC (human)	P41225 (TFClass)
UniProt AC (mouse)	P53784 (TFClass)
GRECO-DB-TF	yes

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

PCM	SOX3.H12INVIVO.0.PM.A.pcm
PWM	SOX3.H12INVIVO.0.PM.A.pwm
PFM	SOX3.H12INVIVO.0.PM.A.pfm
Alignment	SOX3.H12INVIVO.0.PM.A.words.tsv
Threshold to P-value map	SOX3.H12INVIVO.0.PM.A.thr
Motif in other formats
JASPAR format	SOX3.H12INVIVO.0.PM.A_jaspar_format.txt
MEME format	SOX3.H12INVIVO.0.PM.A_meme_format.meme
Transfac format	SOX3.H12INVIVO.0.PM.A_transfac_format.txt
Homer format	SOX3.H12INVIVO.0.PM.A_homer_format_0.001.txt SOX3.H12INVIVO.0.PM.A_homer_format_0.0005.txt SOX3.H12INVIVO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	61.0	325.0	359.0	271.0
02	15.0	728.0	118.0	155.0
03	19.0	679.0	7.0	311.0
04	384.0	6.0	2.0	624.0
05	1.0	4.0	2.0	1009.0
06	0.0	0.0	3.0	1013.0
07	24.0	29.0	961.0	2.0
08	19.0	7.0	8.0	982.0
09	13.0	324.0	159.0	520.0
10	204.0	458.0	121.0	233.0
11	103.0	298.0	154.0	461.0
12	121.0	304.0	374.0	217.0

PFM

	A	C	G	T
01	0.06	0.32	0.353	0.267
02	0.015	0.717	0.116	0.153
03	0.019	0.668	0.007	0.306
04	0.378	0.006	0.002	0.614
05	0.001	0.004	0.002	0.993
06	0.0	0.0	0.003	0.997
07	0.024	0.029	0.946	0.002
08	0.019	0.007	0.008	0.967
09	0.013	0.319	0.156	0.512
10	0.201	0.451	0.119	0.229
11	0.101	0.293	0.152	0.454
12	0.119	0.299	0.368	0.214

PWM

	A	C	G	T
01	-1.405	0.245	0.344	0.064
02	-2.727	1.049	-0.759	-0.49
03	-2.513	0.979	-3.377	0.201
04	0.411	-3.499	-4.227	0.895
05	-4.539	-3.798	-4.227	1.374
06	-4.995	-4.995	-3.99	1.378
07	-2.296	-2.119	1.326	-4.227
08	-2.513	-3.377	-3.269	1.347
09	-2.854	0.242	-0.464	0.713
10	-0.218	0.587	-0.734	-0.086
11	-0.893	0.159	-0.496	0.593
12	-0.734	0.179	0.385	-0.156

Standard thresholds

P-value	Threshold
0.001	4.274915
0.0005	5.37684
0.0001	7.63211