SOX18.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX18.H12INVITRO.0.SM.B
Gene (human)	SOX18 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox18
Gene synonyms (mouse)	Sox-18
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	9
Consensus	nGCATTGTb
GC content	44.68%
Information content (bits; total / per base)	13.13 / 1.459
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	4038

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.774	0.737	0.72	0.689	0.664	0.643
Overall, 2 experiments	best	0.936	0.898	0.857	0.821	0.772	0.744
Methyl HT-SELEX, 1 experiments	median	0.936	0.898	0.857	0.821	0.772	0.744
Methyl HT-SELEX, 1 experiments	best	0.936	0.898	0.857	0.821	0.772	0.744
Non-Methyl HT-SELEX, 1 experiments	median	0.613	0.577	0.582	0.556	0.555	0.541
Non-Methyl HT-SELEX, 1 experiments	best	0.613	0.577	0.582	0.556	0.555	0.541

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.554	0.168	0.521	0.349

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: 4.1.1.6.3
HGNC	HGNC:11194
MGI	MGI:103559
EntrezGene (human)	GeneID:54345 (SSTAR profile)
EntrezGene (mouse)	GeneID:20672 (SSTAR profile)
UniProt ID (human)	SOX18_HUMAN
UniProt ID (mouse)	SOX18_MOUSE
UniProt AC (human)	P35713 (TFClass)
UniProt AC (mouse)	P43680 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	SOX18.H12INVITRO.0.SM.B.pcm
PWM	SOX18.H12INVITRO.0.SM.B.pwm
PFM	SOX18.H12INVITRO.0.SM.B.pfm
Alignment	SOX18.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	SOX18.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	SOX18.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	SOX18.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	SOX18.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	SOX18.H12INVITRO.0.SM.B_homer_format_0.001.txt SOX18.H12INVITRO.0.SM.B_homer_format_0.0005.txt SOX18.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	763.0	1008.0	1147.0	1120.0
02	0.0	1669.0	2369.0	0.0
03	0.0	4038.0	0.0	0.0
04	4038.0	0.0	0.0	0.0
05	0.0	0.0	0.0	4038.0
06	0.0	0.0	0.0	4038.0
07	0.0	0.0	4038.0	0.0
08	0.0	0.0	0.0	4038.0
09	542.5	1087.5	880.5	1527.5

PFM

	A	C	G	T
01	0.189	0.25	0.284	0.277
02	0.0	0.413	0.587	0.0
03	0.0	1.0	0.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.134	0.269	0.218	0.378

PWM

	A	C	G	T
01	-0.279	-0.001	0.127	0.104
02	-6.189	0.502	0.852	-6.189
03	-6.189	1.385	-6.189	-6.189
04	1.385	-6.189	-6.189	-6.189
05	-6.189	-6.189	-6.189	1.385
06	-6.189	-6.189	-6.189	1.385
07	-6.189	-6.189	1.385	-6.189
08	-6.189	-6.189	-6.189	1.385
09	-0.619	0.074	-0.136	0.413

Standard thresholds

P-value	Threshold
0.001	1.505545
0.0005	1.77284
0.0001	8.3682