SOX9.H12CORE.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12CORE.1.PS.A
Gene (human)	SOX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox9
Gene synonyms (mouse)	Sox-9
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	10
Consensus	nbhATTGTdn
GC content	34.56%
Information content (bits; total / per base)	10.045 / 1.004
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9295

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	1 (7)	0.539	0.579	0.397	0.449	0.402	0.53	0.983	1.321	17.244	25.092
Mouse	6 (41)	0.622	0.721	0.455	0.563	0.59	0.718	1.461	1.977	50.208	230.237

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.734	0.705	0.665	0.652	0.593	0.597
Non-Methyl HT-SELEX, 4 experiments	best	0.91	0.878	0.825	0.783	0.749	0.716

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.743	0.438	0.737	0.633

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: 4.1.1.5.2
HGNC	HGNC:11204
MGI	MGI:98371
EntrezGene (human)	GeneID:6662 (SSTAR profile)
EntrezGene (mouse)	GeneID:20682 (SSTAR profile)
UniProt ID (human)	SOX9_HUMAN
UniProt ID (mouse)	SOX9_MOUSE
UniProt AC (human)	P48436 (TFClass)
UniProt AC (mouse)	Q04887 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 6 mouse
HT-SELEX	4
Methyl-HT-SELEX	0

PCM	SOX9.H12CORE.1.PS.A.pcm
PWM	SOX9.H12CORE.1.PS.A.pwm
PFM	SOX9.H12CORE.1.PS.A.pfm
Alignment	SOX9.H12CORE.1.PS.A.words.tsv
Threshold to P-value map	SOX9.H12CORE.1.PS.A.thr
Motif in other formats
JASPAR format	SOX9.H12CORE.1.PS.A_jaspar_format.txt
MEME format	SOX9.H12CORE.1.PS.A_meme_format.meme
Transfac format	SOX9.H12CORE.1.PS.A_transfac_format.txt
Homer format	SOX9.H12CORE.1.PS.A_homer_format_0.001.txt SOX9.H12CORE.1.PS.A_homer_format_0.0005.txt SOX9.H12CORE.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2027.0	2281.0	2356.0	2631.0
02	910.75	3687.75	2326.75	2369.75
03	1160.0	4059.0	625.0	3451.0
04	9029.0	20.0	44.0	202.0
05	0.0	2.0	4.0	9289.0
06	0.0	0.0	0.0	9295.0
07	37.0	33.0	9225.0	0.0
08	798.0	16.0	13.0	8468.0
09	1341.0	1262.0	1673.0	5019.0
10	1684.5	2841.5	1650.5	3118.5

PFM

	A	C	G	T
01	0.218	0.245	0.253	0.283
02	0.098	0.397	0.25	0.255
03	0.125	0.437	0.067	0.371
04	0.971	0.002	0.005	0.022
05	0.0	0.0	0.0	0.999
06	0.0	0.0	0.0	1.0
07	0.004	0.004	0.992	0.0
08	0.086	0.002	0.001	0.911
09	0.144	0.136	0.18	0.54
10	0.181	0.306	0.178	0.336

PWM

	A	C	G	T
01	-0.136	-0.019	0.014	0.124
02	-0.935	0.461	0.001	0.02
03	-0.694	0.557	-1.311	0.395
04	1.357	-4.648	-3.917	-2.432
05	-6.926	-6.297	-5.914	1.385
06	-6.926	-6.926	-6.926	1.386
07	-4.081	-4.188	1.378	-6.926
08	-1.067	-4.846	-5.025	1.292
09	-0.549	-0.61	-0.328	0.77
10	-0.321	0.201	-0.342	0.294

Standard thresholds

P-value	Threshold
0.001	4.971435
0.0005	6.24514
0.0001	7.62301