SOX2.H12INVITRO.3.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX2.H12INVITRO.3.S.B
Gene (human)	SOX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox2
Gene synonyms (mouse)	Sox-2
LOGO
LOGO (reverse complement)
Motif subtype	3
Quality	B

Motif length	12
Consensus	RWTdhCATTCWn
GC content	28.3%
Information content (bits; total / per base)	12.843 / 1.07
Data sources	HT-SELEX
Aligned words	1366

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)	0.569	0.69	0.373	0.479	0.595	0.771	1.362	2.361	2.81	27.041
Mouse	116 (745)	0.589	0.682	0.392	0.495	0.57	0.732	1.269	2.017	5.347	26.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 5 experiments	median	0.674	0.649	0.603	0.59	0.561	0.558
Non-Methyl HT-SELEX, 5 experiments	best	0.712	0.699	0.625	0.618	0.572	0.574

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.3.S.B.pcm
PWM	SOX2.H12INVITRO.3.S.B.pwm
PFM	SOX2.H12INVITRO.3.S.B.pfm
Alignment	SOX2.H12INVITRO.3.S.B.words.tsv
Threshold to P-value map	SOX2.H12INVITRO.3.S.B.thr
Motif in other formats
JASPAR format	SOX2.H12INVITRO.3.S.B_jaspar_format.txt
MEME format	SOX2.H12INVITRO.3.S.B_meme_format.meme
Transfac format	SOX2.H12INVITRO.3.S.B_transfac_format.txt
Homer format	SOX2.H12INVITRO.3.S.B_homer_format_0.001.txt SOX2.H12INVITRO.3.S.B_homer_format_0.0005.txt SOX2.H12INVITRO.3.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1052.75	94.75	114.75	103.75
02	998.75	97.75	86.75	182.75
03	82.0	41.0	78.0	1165.0
04	706.0	76.0	167.0	417.0
05	530.0	228.0	185.0	423.0
06	18.0	1342.0	0.0	6.0
07	1366.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1366.0
09	0.0	0.0	0.0	1366.0
10	2.0	1014.0	341.0	9.0
11	835.25	74.25	125.25	331.25
12	339.5	349.5	224.5	452.5

PFM

	A	C	G	T
01	0.771	0.069	0.084	0.076
02	0.731	0.072	0.064	0.134
03	0.06	0.03	0.057	0.853
04	0.517	0.056	0.122	0.305
05	0.388	0.167	0.135	0.31
06	0.013	0.982	0.0	0.004
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.0	1.0
10	0.001	0.742	0.25	0.007
11	0.611	0.054	0.092	0.242
12	0.249	0.256	0.164	0.331

PWM

	A	C	G	T
01	1.122	-1.269	-1.08	-1.179
02	1.07	-1.238	-1.355	-0.621
03	-1.41	-2.082	-1.459	1.223
04	0.724	-1.484	-0.71	0.199
05	0.438	-0.401	-0.609	0.213
06	-2.853	1.365	-5.248	-3.784
07	1.382	-5.248	-5.248	-5.248
08	-5.248	-5.248	-5.248	1.382
09	-5.248	-5.248	-5.248	1.382
10	-4.502	1.085	-0.001	-3.459
11	0.891	-1.507	-0.994	-0.03
12	-0.006	0.023	-0.417	0.28

Standard thresholds

P-value	Threshold
0.001	3.559265
0.0005	4.85367
0.0001	7.26355