SOX9.H12CORE.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12CORE.0.PS.A
Gene (human)	SOX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox9
Gene synonyms (mouse)	Sox-9
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	21
Consensus	ddhhMWdddnbYATTGTTYbn
GC content	36.78%
Information content (bits; total / per base)	15.148 / 0.721
Data sources	ChIP-Seq + HT-SELEX
Aligned words	2500

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)	0.535	0.583	0.42	0.488	0.422	0.58	1.258	1.727	27.699	40.959
Mouse	6 (41)	0.665	0.818	0.512	0.701	0.676	0.849	2.036	3.065	92.553	306.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.727	0.706	0.639	0.631	0.576	0.581
Non-Methyl HT-SELEX, 4 experiments	best	0.915	0.897	0.784	0.772	0.669	0.676

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.67	0.38	0.699	0.534

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.0.PS.A.pcm
PWM	SOX9.H12CORE.0.PS.A.pwm
PFM	SOX9.H12CORE.0.PS.A.pfm
Alignment	SOX9.H12CORE.0.PS.A.words.tsv
Threshold to P-value map	SOX9.H12CORE.0.PS.A.thr
Motif in other formats
JASPAR format	SOX9.H12CORE.0.PS.A_jaspar_format.txt
MEME format	SOX9.H12CORE.0.PS.A_meme_format.meme
Transfac format	SOX9.H12CORE.0.PS.A_transfac_format.txt
Homer format	SOX9.H12CORE.0.PS.A_homer_format_0.001.txt SOX9.H12CORE.0.PS.A_homer_format_0.0005.txt SOX9.H12CORE.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	982.0	342.0	618.0	558.0
02	1318.5	255.5	488.5	437.5
03	1238.0	616.0	297.0	349.0
04	1128.0	897.0	212.0	263.0
05	1538.0	514.0	181.0	267.0
06	1403.0	248.0	170.0	679.0
07	898.0	139.0	424.0	1039.0
08	648.0	175.0	891.0	786.0
09	574.0	322.0	1061.0	543.0
10	393.0	551.0	904.0	652.0
11	117.0	1254.0	582.0	547.0
12	198.0	1059.0	75.0	1168.0
13	2460.0	9.0	13.0	18.0
14	4.0	2.0	22.0	2472.0
15	0.0	2.0	6.0	2492.0
16	1.0	3.0	2496.0	0.0
17	10.0	7.0	2.0	2481.0
18	77.0	51.0	42.0	2330.0
19	302.0	1616.0	135.0	447.0
20	346.75	461.75	842.75	848.75
21	463.75	659.75	662.75	713.75

PFM

	A	C	G	T
01	0.393	0.137	0.247	0.223
02	0.527	0.102	0.195	0.175
03	0.495	0.246	0.119	0.14
04	0.451	0.359	0.085	0.105
05	0.615	0.206	0.072	0.107
06	0.561	0.099	0.068	0.272
07	0.359	0.056	0.17	0.416
08	0.259	0.07	0.356	0.314
09	0.23	0.129	0.424	0.217
10	0.157	0.22	0.362	0.261
11	0.047	0.502	0.233	0.219
12	0.079	0.424	0.03	0.467
13	0.984	0.004	0.005	0.007
14	0.002	0.001	0.009	0.989
15	0.0	0.001	0.002	0.997
16	0.0	0.001	0.998	0.0
17	0.004	0.003	0.001	0.992
18	0.031	0.02	0.017	0.932
19	0.121	0.646	0.054	0.179
20	0.139	0.185	0.337	0.34
21	0.186	0.264	0.265	0.286

PWM

	A	C	G	T
01	0.451	-0.6	-0.011	-0.113
02	0.745	-0.89	-0.246	-0.355
03	0.682	-0.014	-0.741	-0.58
04	0.589	0.36	-1.075	-0.861
05	0.899	-0.195	-1.232	-0.846
06	0.807	-0.92	-1.294	0.083
07	0.361	-1.492	-0.387	0.507
08	0.036	-1.265	0.354	0.229
09	-0.085	-0.66	0.528	-0.14
10	-0.462	-0.126	0.368	0.042
11	-1.662	0.695	-0.071	-0.133
12	-1.143	0.526	-2.098	0.624
13	1.368	-4.047	-3.736	-3.447
14	-4.656	-5.066	-3.265	1.373
15	-5.77	-5.066	-4.367	1.381
16	-5.357	-4.84	1.382	-5.77
17	-3.96	-4.249	-5.066	1.376
18	-2.072	-2.471	-2.658	1.314
19	-0.724	0.948	-1.521	-0.334
20	-0.587	-0.302	0.298	0.305
21	-0.297	0.054	0.058	0.132

Standard thresholds

P-value	Threshold
0.001	2.23796
0.0005	3.60411
0.0001	6.45241