SOX9.H12RSNP.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12RSNP.2.S.B
Gene (human)	SOX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox9
Gene synonyms (mouse)	Sox-9
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	17
Consensus	nMWvAATTKCAGTSWKn
GC content	34.09%
Information content (bits; total / per base)	16.876 / 0.993
Data sources	HT-SELEX
Aligned words	1627

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)	0.463	0.484	0.304	0.321	0.343	0.542	0.682	1.236	0	0.027
Mouse	6 (41)	0.476	0.515	0.319	0.355	0.52	0.576	1.089	1.26	0	1.119

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.649	0.643	0.58	0.58	0.547	0.55
Non-Methyl HT-SELEX, 4 experiments	best	0.713	0.701	0.623	0.617	0.575	0.575

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.624	0.208	0.602	0.426

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.H12RSNP.2.S.B.pcm
PWM	SOX9.H12RSNP.2.S.B.pwm
PFM	SOX9.H12RSNP.2.S.B.pfm
Alignment	SOX9.H12RSNP.2.S.B.words.tsv
Threshold to P-value map	SOX9.H12RSNP.2.S.B.thr
Motif in other formats
JASPAR format	SOX9.H12RSNP.2.S.B_jaspar_format.txt
MEME format	SOX9.H12RSNP.2.S.B_meme_format.meme
Transfac format	SOX9.H12RSNP.2.S.B_transfac_format.txt
Homer format	SOX9.H12RSNP.2.S.B_homer_format_0.001.txt SOX9.H12RSNP.2.S.B_homer_format_0.0005.txt SOX9.H12RSNP.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	639.0	263.0	356.0	369.0
02	1022.5	245.5	207.5	151.5
03	468.0	67.0	86.0	1006.0
04	338.0	635.0	622.0	32.0
05	1568.0	26.0	11.0	22.0
06	1488.0	28.0	22.0	89.0
07	49.0	9.0	59.0	1510.0
08	15.0	16.0	122.0	1474.0
09	65.0	97.0	767.0	698.0
10	15.0	1489.0	3.0	120.0
11	1588.0	22.0	11.0	6.0
12	6.0	10.0	1560.0	51.0
13	4.0	12.0	40.0	1571.0
14	18.0	688.0	682.0	239.0
15	1084.0	45.0	32.0	466.0
16	105.5	236.5	278.5	1006.5
17	463.75	258.75	422.75	481.75

PFM

	A	C	G	T
01	0.393	0.162	0.219	0.227
02	0.628	0.151	0.128	0.093
03	0.288	0.041	0.053	0.618
04	0.208	0.39	0.382	0.02
05	0.964	0.016	0.007	0.014
06	0.915	0.017	0.014	0.055
07	0.03	0.006	0.036	0.928
08	0.009	0.01	0.075	0.906
09	0.04	0.06	0.471	0.429
10	0.009	0.915	0.002	0.074
11	0.976	0.014	0.007	0.004
12	0.004	0.006	0.959	0.031
13	0.002	0.007	0.025	0.966
14	0.011	0.423	0.419	0.147
15	0.666	0.028	0.02	0.286
16	0.065	0.145	0.171	0.619
17	0.285	0.159	0.26	0.296

PWM

	A	C	G	T
01	0.45	-0.434	-0.133	-0.097
02	0.919	-0.502	-0.669	-0.98
03	0.14	-1.781	-1.537	0.903
04	-0.184	0.444	0.423	-2.491
05	1.346	-2.686	-3.459	-2.841
06	1.294	-2.617	-2.841	-1.504
07	-2.084	-3.629	-1.904	1.308
08	-3.188	-3.131	-1.194	1.284
09	-1.81	-1.419	0.632	0.538
10	-3.188	1.294	-4.434	-1.21
11	1.359	-2.841	-3.459	-3.952
12	-3.952	-3.541	1.341	-2.045
13	-4.247	-3.385	-2.279	1.348
14	-3.025	0.524	0.515	-0.529
15	0.977	-2.166	-2.491	0.135
16	-1.337	-0.539	-0.377	0.903
17	0.131	-0.45	0.038	0.169

Standard thresholds

P-value	Threshold
0.001	1.94251
0.0005	3.22351
0.0001	5.91711