SOX8.H12RSNP.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX8.H12RSNP.1.PS.A
Gene (human)	SOX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox8
Gene synonyms (mouse)	Sox-8
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	11
Consensus	bYCWTTGTYbb
GC content	41.89%
Information content (bits; total / per base)	9.844 / 0.895
Data sources	ChIP-Seq + HT-SELEX
Aligned words	973

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	3 (15)	0.695	0.738	0.554	0.585	0.728	0.764	1.977	2.129	67.208	99.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.979	0.962	0.969	0.949	0.936	0.915
Overall, 4 experiments	best	0.992	0.982	0.99	0.981	0.984	0.974
Methyl HT-SELEX, 2 experiments	median	0.98	0.963	0.971	0.953	0.943	0.924
Methyl HT-SELEX, 2 experiments	best	0.992	0.982	0.99	0.981	0.984	0.974
Non-Methyl HT-SELEX, 2 experiments	median	0.969	0.949	0.937	0.916	0.868	0.857
Non-Methyl HT-SELEX, 2 experiments	best	0.989	0.981	0.985	0.974	0.971	0.957

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.738	0.51	0.746	0.511

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 E {4.1.1.5} (TFClass)
TFClass ID	TFClass: 4.1.1.5.1
HGNC	HGNC:11203
MGI	MGI:98370
EntrezGene (human)	GeneID:30812 (SSTAR profile)
EntrezGene (mouse)	GeneID:20681 (SSTAR profile)
UniProt ID (human)	SOX8_HUMAN
UniProt ID (mouse)	SOX8_MOUSE
UniProt AC (human)	P57073 (TFClass)
UniProt AC (mouse)	Q04886 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SOX8.H12RSNP.1.PS.A.pcm
PWM	SOX8.H12RSNP.1.PS.A.pwm
PFM	SOX8.H12RSNP.1.PS.A.pfm
Alignment	SOX8.H12RSNP.1.PS.A.words.tsv
Threshold to P-value map	SOX8.H12RSNP.1.PS.A.thr
Motif in other formats
JASPAR format	SOX8.H12RSNP.1.PS.A_jaspar_format.txt
MEME format	SOX8.H12RSNP.1.PS.A_meme_format.meme
Transfac format	SOX8.H12RSNP.1.PS.A_transfac_format.txt
Homer format	SOX8.H12RSNP.1.PS.A_homer_format_0.001.txt SOX8.H12RSNP.1.PS.A_homer_format_0.0005.txt SOX8.H12RSNP.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	49.0	309.0	298.0	317.0
02	35.0	539.0	145.0	254.0
03	53.0	760.0	4.0	156.0
04	362.0	67.0	11.0	533.0
05	3.0	87.0	17.0	866.0
06	2.0	3.0	2.0	966.0
07	19.0	54.0	891.0	9.0
08	24.0	5.0	2.0	942.0
09	30.0	229.0	183.0	531.0
10	75.0	373.0	86.0	439.0
11	141.0	266.0	153.0	413.0

PFM

	A	C	G	T
01	0.05	0.318	0.306	0.326
02	0.036	0.554	0.149	0.261
03	0.054	0.781	0.004	0.16
04	0.372	0.069	0.011	0.548
05	0.003	0.089	0.017	0.89
06	0.002	0.003	0.002	0.993
07	0.02	0.055	0.916	0.009
08	0.025	0.005	0.002	0.968
09	0.031	0.235	0.188	0.546
10	0.077	0.383	0.088	0.451
11	0.145	0.273	0.157	0.424

PWM

	A	C	G	T
01	-1.575	0.238	0.202	0.263
02	-1.898	0.792	-0.513	0.043
03	-1.499	1.134	-3.757	-0.44
04	0.395	-1.271	-2.958	0.781
05	-3.949	-1.016	-2.572	1.265
06	-4.187	-3.949	-4.187	1.374
07	-2.47	-1.481	1.293	-3.129
08	-2.254	-3.596	-4.187	1.349
09	-2.044	-0.06	-0.282	0.777
10	-1.161	0.425	-1.027	0.587
11	-0.54	0.089	-0.46	0.526

Standard thresholds

P-value	Threshold
0.001	4.812645
0.0005	5.7264
0.0001	7.431445