SOX2.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX2.H12INVITRO.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	bbbCATTSTbnh
GC content	39.13%
Information content (bits; total / per base)	8.884 / 0.74
Data sources	ChIP-Seq
Aligned words	164

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)	0.756	0.837	0.606	0.687	0.794	0.854	2.281	2.615	75.828	182.921
Mouse	116 (745)	0.758	0.851	0.578	0.708	0.791	0.865	2.214	2.799	74.244	197.31

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 5 experiments	median	0.596	0.563	0.568	0.546	0.548	0.534
Non-Methyl HT-SELEX, 5 experiments	best	0.612	0.573	0.584	0.555	0.557	0.541

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.H12INVITRO.0.P.B.pcm
PWM	SOX2.H12INVITRO.0.P.B.pwm
PFM	SOX2.H12INVITRO.0.P.B.pfm
Alignment	SOX2.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	SOX2.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	SOX2.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	SOX2.H12INVITRO.0.P.B_meme_format.meme
Transfac format	SOX2.H12INVITRO.0.P.B_transfac_format.txt
Homer format	SOX2.H12INVITRO.0.P.B_homer_format_0.001.txt SOX2.H12INVITRO.0.P.B_homer_format_0.0005.txt SOX2.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	25.0	33.0	28.0	78.0
02	12.0	26.0	41.0	85.0
03	11.0	76.0	37.0	40.0
04	9.0	134.0	5.0	16.0
05	101.0	0.0	0.0	63.0
06	1.0	3.0	2.0	158.0
07	2.0	0.0	2.0	160.0
08	4.0	26.0	124.0	10.0
09	14.0	4.0	1.0	145.0
10	22.0	43.0	32.0	67.0
11	34.0	59.0	26.0	45.0
12	33.0	44.0	24.0	63.0

PFM

	A	C	G	T
01	0.152	0.201	0.171	0.476
02	0.073	0.159	0.25	0.518
03	0.067	0.463	0.226	0.244
04	0.055	0.817	0.03	0.098
05	0.616	0.0	0.0	0.384
06	0.006	0.018	0.012	0.963
07	0.012	0.0	0.012	0.976
08	0.024	0.159	0.756	0.061
09	0.085	0.024	0.006	0.884
10	0.134	0.262	0.195	0.409
11	0.207	0.36	0.159	0.274
12	0.201	0.268	0.146	0.384

PWM

	A	C	G	T
01	-0.476	-0.21	-0.367	0.629
02	-1.158	-0.438	0.0	0.713
03	-1.237	0.603	-0.099	-0.024
04	-1.414	1.163	-1.908	-0.895
05	0.883	-3.501	-3.501	0.419
06	-2.922	-2.291	-2.558	1.326
07	-2.558	-3.501	-2.558	1.339
08	-2.081	-0.438	1.086	-1.322
09	-1.018	-2.081	-2.922	1.241
10	-0.597	0.046	-0.239	0.479
11	-0.181	0.355	-0.438	0.09
12	-0.21	0.069	-0.514	0.419

Standard thresholds

P-value	Threshold
0.001	5.03076
0.0005	5.772825
0.0001	7.233465