SOX2.H12RSNP.1.P.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX2.H12RSNP.1.P.D
Gene (human)	SOX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox2
Gene synonyms (mouse)	Sox-2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	17
Consensus	bSYWTTGThhTKYhdWh
GC content	37.14%
Information content (bits; total / per base)	12.706 / 0.747
Data sources	ChIP-Seq
Aligned words	1002

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)	0.696	0.911	0.545	0.86	0.756	0.934	2.259	4.897	57.523	315.538
Mouse	116 (745)	0.807	0.948	0.729	0.923	0.833	0.958	3.076	5.639	101.959	626.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 5 experiments	median	0.547	0.528	0.534	0.522	0.521	0.516
Non-Methyl HT-SELEX, 5 experiments	best	0.568	0.54	0.55	0.531	0.535	0.523

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.H12RSNP.1.P.D.pcm
PWM	SOX2.H12RSNP.1.P.D.pwm
PFM	SOX2.H12RSNP.1.P.D.pfm
Alignment	SOX2.H12RSNP.1.P.D.words.tsv
Threshold to P-value map	SOX2.H12RSNP.1.P.D.thr
Motif in other formats
JASPAR format	SOX2.H12RSNP.1.P.D_jaspar_format.txt
MEME format	SOX2.H12RSNP.1.P.D_meme_format.meme
Transfac format	SOX2.H12RSNP.1.P.D_transfac_format.txt
Homer format	SOX2.H12RSNP.1.P.D_homer_format_0.001.txt SOX2.H12RSNP.1.P.D_homer_format_0.0005.txt SOX2.H12RSNP.1.P.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	100.0	243.0	281.0	378.0
02	35.0	636.0	166.0	165.0
03	24.0	632.0	26.0	320.0
04	524.0	6.0	4.0	468.0
05	2.0	2.0	12.0	986.0
06	12.0	1.0	5.0	984.0
07	39.0	138.0	803.0	22.0
08	136.0	3.0	4.0	859.0
09	124.0	258.0	120.0	500.0
10	560.0	238.0	70.0	134.0
11	57.0	79.0	42.0	824.0
12	50.0	95.0	694.0	163.0
13	66.0	604.0	147.0	185.0
14	558.0	124.0	68.0	252.0
15	543.0	101.0	190.0	168.0
16	650.0	131.0	86.0	135.0
17	210.0	161.0	157.0	474.0

PFM

	A	C	G	T
01	0.1	0.243	0.28	0.377
02	0.035	0.635	0.166	0.165
03	0.024	0.631	0.026	0.319
04	0.523	0.006	0.004	0.467
05	0.002	0.002	0.012	0.984
06	0.012	0.001	0.005	0.982
07	0.039	0.138	0.801	0.022
08	0.136	0.003	0.004	0.857
09	0.124	0.257	0.12	0.499
10	0.559	0.238	0.07	0.134
11	0.057	0.079	0.042	0.822
12	0.05	0.095	0.693	0.163
13	0.066	0.603	0.147	0.185
14	0.557	0.124	0.068	0.251
15	0.542	0.101	0.19	0.168
16	0.649	0.131	0.086	0.135
17	0.21	0.161	0.157	0.473

PWM

	A	C	G	T
01	-0.908	-0.03	0.114	0.409
02	-1.927	0.928	-0.408	-0.414
03	-2.283	0.921	-2.208	0.243
04	0.734	-3.486	-3.785	0.622
05	-4.215	-4.215	-2.911	1.365
06	-2.911	-4.527	-3.624	1.363
07	-1.823	-0.591	1.16	-2.364
08	-0.605	-3.977	-3.785	1.227
09	-0.696	0.029	-0.729	0.688
10	0.801	-0.051	-1.257	-0.62
11	-1.457	-1.139	-1.752	1.186
12	-1.584	-0.958	1.015	-0.426
13	-1.315	0.876	-0.528	-0.301
14	0.797	-0.696	-1.286	0.006
15	0.77	-0.898	-0.274	-0.396
16	0.949	-0.642	-1.056	-0.612
17	-0.175	-0.438	-0.463	0.635

Standard thresholds

P-value	Threshold
0.001	4.01841
0.0005	5.02746
0.0001	7.08256