SOX9.H12INVIVO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12INVIVO.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	11
Consensus	bbCWTTGTKYh
GC content	44.55%
Information content (bits; total / per base)	10.895 / 0.99
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1004

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)	0.528	0.588	0.416	0.477	0.487	0.561	1.235	1.462	9.921	26.886
Mouse	6 (41)	0.698	0.869	0.568	0.754	0.715	0.88	2.085	3.003	79.18	370.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.677	0.638	0.626	0.6	0.581	0.569
Non-Methyl HT-SELEX, 4 experiments	best	0.843	0.787	0.754	0.712	0.667	0.648

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.583	0.279	0.673	0.498

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.H12INVIVO.1.PS.A.pcm
PWM	SOX9.H12INVIVO.1.PS.A.pwm
PFM	SOX9.H12INVIVO.1.PS.A.pfm
Alignment	SOX9.H12INVIVO.1.PS.A.words.tsv
Threshold to P-value map	SOX9.H12INVIVO.1.PS.A.thr
Motif in other formats
JASPAR format	SOX9.H12INVIVO.1.PS.A_jaspar_format.txt
MEME format	SOX9.H12INVIVO.1.PS.A_meme_format.meme
Transfac format	SOX9.H12INVIVO.1.PS.A_transfac_format.txt
Homer format	SOX9.H12INVIVO.1.PS.A_homer_format_0.001.txt SOX9.H12INVIVO.1.PS.A_homer_format_0.0005.txt SOX9.H12INVIVO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	97.0	328.0	330.0	249.0
02	33.0	514.0	194.0	263.0
03	5.0	918.0	8.0	73.0
04	332.0	67.0	3.0	602.0
05	2.0	81.0	30.0	891.0
06	0.0	1.0	2.0	1001.0
07	15.0	5.0	984.0	0.0
08	4.0	4.0	2.0	994.0
09	50.0	131.0	241.0	582.0
10	73.0	591.0	68.0	272.0
11	204.0	270.0	148.0	382.0

PFM

	A	C	G	T
01	0.097	0.327	0.329	0.248
02	0.033	0.512	0.193	0.262
03	0.005	0.914	0.008	0.073
04	0.331	0.067	0.003	0.6
05	0.002	0.081	0.03	0.887
06	0.0	0.001	0.002	0.997
07	0.015	0.005	0.98	0.0
08	0.004	0.004	0.002	0.99
09	0.05	0.13	0.24	0.58
10	0.073	0.589	0.068	0.271
11	0.203	0.269	0.147	0.38

PWM

	A	C	G	T
01	-0.94	0.266	0.272	-0.008
02	-1.985	0.713	-0.256	0.046
03	-3.626	1.292	-3.257	-1.218
04	0.278	-1.302	-3.979	0.871
05	-4.216	-1.117	-2.075	1.262
06	-4.985	-4.529	-4.216	1.378
07	-2.715	-3.626	1.361	-4.985
08	-3.787	-3.787	-4.216	1.371
09	-1.586	-0.644	-0.04	0.837
10	-1.218	0.852	-1.288	0.08
11	-0.206	0.072	-0.523	0.418

Standard thresholds

P-value	Threshold
0.001	4.465765
0.0005	5.516985
0.0001	7.5508