SOX3.H12CORE.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H12CORE.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	11
Consensus	nSYATTGTYhn
GC content	37.53%
Information content (bits; total / per base)	11.904 / 1.082
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	9972

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)	0.725	0.748	0.557	0.583	0.756	0.782	2.014	2.164	11.409	49.027
Mouse	3 (11)	0.796	0.815	0.638	0.679	0.794	0.809	2.319	2.457	84.553	168.18

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.978	0.963	0.968	0.949	0.925	0.905
Overall, 2 experiments	best	0.989	0.98	0.982	0.97	0.958	0.943
Methyl HT-SELEX, 1 experiments	median	0.989	0.98	0.982	0.97	0.958	0.943
Methyl HT-SELEX, 1 experiments	best	0.989	0.98	0.982	0.97	0.958	0.943
Non-Methyl HT-SELEX, 1 experiments	median	0.968	0.947	0.954	0.927	0.893	0.868
Non-Methyl HT-SELEX, 1 experiments	best	0.968	0.947	0.954	0.927	0.893	0.868

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.628	0.319	0.529	0.383

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.H12CORE.0.PM.A.pcm
PWM	SOX3.H12CORE.0.PM.A.pwm
PFM	SOX3.H12CORE.0.PM.A.pfm
Alignment	SOX3.H12CORE.0.PM.A.words.tsv
Threshold to P-value map	SOX3.H12CORE.0.PM.A.thr
Motif in other formats
JASPAR format	SOX3.H12CORE.0.PM.A_jaspar_format.txt
MEME format	SOX3.H12CORE.0.PM.A_meme_format.meme
Transfac format	SOX3.H12CORE.0.PM.A_transfac_format.txt
Homer format	SOX3.H12CORE.0.PM.A_homer_format_0.001.txt SOX3.H12CORE.0.PM.A_homer_format_0.0005.txt SOX3.H12CORE.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1646.5	2505.5	2879.5	2940.5
02	416.75	5943.75	2171.75	1439.75
03	320.0	5234.0	26.0	4392.0
04	9840.0	3.0	0.0	129.0
05	0.0	0.0	0.0	9972.0
06	0.0	0.0	0.0	9972.0
07	0.0	0.0	9972.0	0.0
08	12.0	1.0	1.0	9958.0
09	631.0	2427.0	835.0	6079.0
10	2468.75	3877.75	1016.75	2608.75
11	2138.25	2563.25	1709.25	3561.25

PFM

	A	C	G	T
01	0.165	0.251	0.289	0.295
02	0.042	0.596	0.218	0.144
03	0.032	0.525	0.003	0.44
04	0.987	0.0	0.0	0.013
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	0.001	0.0	0.0	0.999
09	0.063	0.243	0.084	0.61
10	0.248	0.389	0.102	0.262
11	0.214	0.257	0.171	0.357

PWM

	A	C	G	T
01	-0.414	0.005	0.144	0.165
02	-1.784	0.868	-0.138	-0.548
03	-2.047	0.741	-4.479	0.566
04	1.372	-6.154	-6.988	-2.945
05	-6.988	-6.988	-6.988	1.386
06	-6.988	-6.988	-6.988	1.386
07	-6.988	-6.988	1.386	-6.988
08	-5.162	-6.628	-6.628	1.384
09	-1.371	-0.027	-1.092	0.891
10	-0.01	0.441	-0.896	0.045
11	-0.153	0.028	-0.377	0.356

Standard thresholds

P-value	Threshold
0.001	2.4868
0.0005	4.90887
0.0001	7.852025