SOX17.H12INVIVO.2.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX17.H12INVIVO.2.S.C
Gene (human)	SOX17 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox17
Gene synonyms (mouse)	Sox-17
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	18
Consensus	nMACAATWnCATTGTKnn
GC content	30.32%
Information content (bits; total / per base)	22.079 / 1.227
Data sources	HT-SELEX
Aligned words	579

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	5 (31)	0.539	0.553	0.372	0.393	0.538	0.558	1.197	1.291	4.398	6.854
Mouse	2 (10)	0.513	0.524	0.361	0.371	0.471	0.499	1.075	1.151	9.83	12.155

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.599	0.594	0.55	0.551	0.527	0.531
Non-Methyl HT-SELEX, 2 experiments	best	0.626	0.624	0.562	0.567	0.532	0.539

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 F {4.1.1.6} (TFClass)
TFClass ID	TFClass: 4.1.1.6.2
HGNC	HGNC:18122
MGI	MGI:107543
EntrezGene (human)	GeneID:64321 (SSTAR profile)
EntrezGene (mouse)	GeneID:20671 (SSTAR profile)
UniProt ID (human)	SOX17_HUMAN
UniProt ID (mouse)	SOX17_MOUSE
UniProt AC (human)	Q9H6I2 (TFClass)
UniProt AC (mouse)	Q61473 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 2 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	SOX17.H12INVIVO.2.S.C.pcm
PWM	SOX17.H12INVIVO.2.S.C.pwm
PFM	SOX17.H12INVIVO.2.S.C.pfm
Alignment	SOX17.H12INVIVO.2.S.C.words.tsv
Threshold to P-value map	SOX17.H12INVIVO.2.S.C.thr
Motif in other formats
JASPAR format	SOX17.H12INVIVO.2.S.C_jaspar_format.txt
MEME format	SOX17.H12INVIVO.2.S.C_meme_format.meme
Transfac format	SOX17.H12INVIVO.2.S.C_transfac_format.txt
Homer format	SOX17.H12INVIVO.2.S.C_homer_format_0.001.txt SOX17.H12INVIVO.2.S.C_homer_format_0.0005.txt SOX17.H12INVIVO.2.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	182.0	114.0	133.0	150.0
02	365.0	91.0	62.0	61.0
03	556.0	9.0	10.0	4.0
04	6.0	571.0	1.0	1.0
05	579.0	0.0	0.0	0.0
06	572.0	0.0	1.0	6.0
07	0.0	0.0	0.0	579.0
08	216.0	11.0	32.0	320.0
09	105.0	100.0	170.0	204.0
10	16.0	522.0	1.0	40.0
11	579.0	0.0	0.0	0.0
12	0.0	0.0	30.0	549.0
13	0.0	0.0	0.0	579.0
14	0.0	0.0	579.0	0.0
15	10.0	4.0	6.0	559.0
16	60.0	61.0	98.0	360.0
17	156.0	103.0	156.0	164.0
18	168.5	122.5	172.5	115.5

PFM

	A	C	G	T
01	0.314	0.197	0.23	0.259
02	0.63	0.157	0.107	0.105
03	0.96	0.016	0.017	0.007
04	0.01	0.986	0.002	0.002
05	1.0	0.0	0.0	0.0
06	0.988	0.0	0.002	0.01
07	0.0	0.0	0.0	1.0
08	0.373	0.019	0.055	0.553
09	0.181	0.173	0.294	0.352
10	0.028	0.902	0.002	0.069
11	1.0	0.0	0.0	0.0
12	0.0	0.0	0.052	0.948
13	0.0	0.0	0.0	1.0
14	0.0	0.0	1.0	0.0
15	0.017	0.007	0.01	0.965
16	0.104	0.105	0.169	0.622
17	0.269	0.178	0.269	0.283
18	0.291	0.212	0.298	0.199

PWM

	A	C	G	T
01	0.227	-0.236	-0.084	0.035
02	0.918	-0.458	-0.833	-0.849
03	1.338	-2.626	-2.536	-3.265
04	-2.959	1.364	-4.034	-4.034
05	1.378	-4.522	-4.522	-4.522
06	1.366	-4.522	-4.034	-2.959
07	-4.522	-4.522	-4.522	1.378
08	0.397	-2.453	-1.472	0.787
09	-0.317	-0.365	0.159	0.34
10	-2.119	1.275	-4.034	-1.258
11	1.378	-4.522	-4.522	-4.522
12	-4.522	-4.522	-1.533	1.325
13	-4.522	-4.522	-4.522	1.378
14	-4.522	-4.522	1.378	-4.522
15	-2.536	-3.265	-2.959	1.343
16	-0.865	-0.849	-0.385	0.905
17	0.074	-0.336	0.074	0.124
18	0.15	-0.165	0.174	-0.223

Standard thresholds

P-value	Threshold
0.001	-2.53614
0.0005	-0.80874
0.0001	2.86266