SOX9.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12INVIVO.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	17
Consensus	vAAdRvnnbCWTTGTKY
GC content	45.14%
Information content (bits; total / per base)	13.988 / 0.823
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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)	0.547	0.607	0.479	0.555	0.457	0.55	1.421	1.913	35.854	56.357
Mouse	6 (41)	0.771	0.964	0.715	0.937	0.783	0.967	3.072	5.305	159.237	572.167

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.68	0.652	0.619	0.601	0.576	0.568
Non-Methyl HT-SELEX, 4 experiments	best	0.818	0.78	0.716	0.689	0.637	0.627

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.643	0.295	0.608	0.477

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.0.PS.A.pcm
PWM	SOX9.H12INVIVO.0.PS.A.pwm
PFM	SOX9.H12INVIVO.0.PS.A.pfm
Alignment	SOX9.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	SOX9.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	SOX9.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	SOX9.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	SOX9.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	SOX9.H12INVIVO.0.PS.A_homer_format_0.001.txt SOX9.H12INVIVO.0.PS.A_homer_format_0.0005.txt SOX9.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	308.0	492.0	162.0	38.0
02	858.0	114.0	22.0	6.0
03	817.0	12.0	111.0	60.0
04	391.0	26.0	287.0	296.0
05	180.0	81.0	642.0	97.0
06	303.0	214.0	432.0	51.0
07	308.0	236.0	330.0	126.0
08	180.0	266.0	345.0	209.0
09	52.0	449.0	259.0	240.0
10	17.0	868.0	34.0	81.0
11	379.0	65.0	7.0	549.0
12	2.0	139.0	82.0	777.0
13	0.0	0.0	2.0	998.0
14	21.0	11.0	968.0	0.0
15	10.0	2.0	2.0	986.0
16	38.0	117.0	211.0	634.0
17	55.0	633.0	52.0	260.0

PFM

	A	C	G	T
01	0.308	0.492	0.162	0.038
02	0.858	0.114	0.022	0.006
03	0.817	0.012	0.111	0.06
04	0.391	0.026	0.287	0.296
05	0.18	0.081	0.642	0.097
06	0.303	0.214	0.432	0.051
07	0.308	0.236	0.33	0.126
08	0.18	0.266	0.345	0.209
09	0.052	0.449	0.259	0.24
10	0.017	0.868	0.034	0.081
11	0.379	0.065	0.007	0.549
12	0.002	0.139	0.082	0.777
13	0.0	0.0	0.002	0.998
14	0.021	0.011	0.968	0.0
15	0.01	0.002	0.002	0.986
16	0.038	0.117	0.211	0.634
17	0.055	0.633	0.052	0.26

PWM

	A	C	G	T
01	0.207	0.674	-0.43	-1.846
02	1.228	-0.777	-2.362	-3.484
03	1.179	-2.909	-0.803	-1.406
04	0.445	-2.206	0.137	0.168
05	-0.326	-1.113	0.939	-0.936
06	0.191	-0.154	0.544	-1.563
07	0.207	-0.057	0.276	-0.678
08	-0.326	0.062	0.32	-0.178
09	-1.544	0.583	0.035	-0.041
10	-2.598	1.24	-1.952	-1.113
11	0.414	-1.328	-3.362	0.783
12	-4.213	-0.582	-1.101	1.129
13	-4.982	-4.982	-4.213	1.379
14	-2.405	-2.985	1.349	-4.982
15	-3.066	-4.213	-4.213	1.367
16	-1.846	-0.752	-0.168	0.926
17	-1.49	0.925	-1.544	0.039

Standard thresholds

P-value	Threshold
0.001	3.38301
0.0005	4.52896
0.0001	6.87301