SOX2.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX2.H12INVIVO.0.P.B
Gene (human)	SOX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox2
Gene synonyms (mouse)	Sox-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	bSYWTTGTYhYb
GC content	39.74%
Information content (bits; total / per base)	11.628 / 0.969
Data sources	ChIP-Seq
Aligned words	1007

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	38 (216)	0.794	0.863	0.656	0.758	0.808	0.868	2.437	2.952	103.321	214.027
Mouse	116 (745)	0.818	0.89	0.682	0.832	0.834	0.908	2.643	3.519	104.959	271.585

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 5 experiments	median	0.565	0.54	0.545	0.529	0.529	0.521
Non-Methyl HT-SELEX, 5 experiments	best	0.578	0.546	0.557	0.536	0.54	0.527

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: 4.1.1.2.2
HGNC	HGNC:11195
MGI	MGI:98364
EntrezGene (human)	GeneID:6657 (SSTAR profile)
EntrezGene (mouse)	GeneID:20674 (SSTAR profile)
UniProt ID (human)	SOX2_HUMAN
UniProt ID (mouse)	SOX2_MOUSE
UniProt AC (human)	P48431 (TFClass)
UniProt AC (mouse)	P48432 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	38 human, 116 mouse
HT-SELEX	5
Methyl-HT-SELEX	0

PCM	SOX2.H12INVIVO.0.P.B.pcm
PWM	SOX2.H12INVIVO.0.P.B.pwm
PFM	SOX2.H12INVIVO.0.P.B.pfm
Alignment	SOX2.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	SOX2.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	SOX2.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	SOX2.H12INVIVO.0.P.B_meme_format.meme
Transfac format	SOX2.H12INVIVO.0.P.B_transfac_format.txt
Homer format	SOX2.H12INVIVO.0.P.B_homer_format_0.001.txt SOX2.H12INVIVO.0.P.B_homer_format_0.0005.txt SOX2.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	71.0	250.0	313.0	373.0
02	13.0	703.0	147.0	144.0
03	11.0	618.0	13.0	365.0
04	497.0	9.0	1.0	500.0
05	1.0	4.0	4.0	998.0
06	2.0	0.0	2.0	1003.0
07	17.0	44.0	941.0	5.0
08	14.0	1.0	2.0	990.0
09	71.0	296.0	87.0	553.0
10	386.0	365.0	84.0	172.0
11	93.0	145.0	63.0	706.0
12	120.0	171.0	539.0	177.0

PFM

	A	C	G	T
01	0.071	0.248	0.311	0.37
02	0.013	0.698	0.146	0.143
03	0.011	0.614	0.013	0.362
04	0.494	0.009	0.001	0.497
05	0.001	0.004	0.004	0.991
06	0.002	0.0	0.002	0.996
07	0.017	0.044	0.934	0.005
08	0.014	0.001	0.002	0.983
09	0.071	0.294	0.086	0.549
10	0.383	0.362	0.083	0.171
11	0.092	0.144	0.063	0.701
12	0.119	0.17	0.535	0.176

PWM

	A	C	G	T
01	-1.249	-0.007	0.216	0.391
02	-2.845	1.023	-0.533	-0.554
03	-2.991	0.894	-2.845	0.369
04	0.677	-3.162	-4.531	0.683
05	-4.531	-3.79	-3.79	1.372
06	-4.219	-4.988	-4.219	1.377
07	-2.605	-1.713	1.313	-3.629
08	-2.78	-4.531	-4.219	1.364
09	-1.249	0.161	-1.05	0.783
10	0.425	0.369	-1.084	-0.378
11	-0.984	-0.547	-1.365	1.027
12	-0.733	-0.384	0.758	-0.349

Standard thresholds

P-value	Threshold
0.001	4.15528
0.0005	5.29547
0.0001	7.489715