SOX9.H13RSNP.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H13RSNP.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	nbhATTGTKn
GC content	34.52%
Information content (bits; total / per base)	11.019 / 1.102
Data sources	ChIP-Seq + HT-SELEX
Aligned words	7326
Previous names	SOX9.H12RSNP.1.PS.A

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)	0.512	0.569	0.389	0.447	0.422	0.538	1.009	1.334	13.328	21.959
Mouse	6 (41)	0.615	0.713	0.455	0.563	0.605	0.727	1.479	1.991	46.569	200.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.73	0.703	0.666	0.651	0.598	0.598
Non-Methyl HT-SELEX, 4 experiments	best	0.908	0.876	0.818	0.777	0.744	0.712

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.734	0.419	0.765	0.627

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SOX9.H13RSNP.1.PS.A.pcm
PWM	SOX9.H13RSNP.1.PS.A.pwm
PFM	SOX9.H13RSNP.1.PS.A.pfm
Threshold to P-value map	SOX9.H13RSNP.1.PS.A.thr
Motif in other formats
JASPAR format	SOX9.H13RSNP.1.PS.A_jaspar_format.txt
MEME format	SOX9.H13RSNP.1.PS.A_meme_format.meme
Transfac format	SOX9.H13RSNP.1.PS.A_transfac_format.txt
Homer format	SOX9.H13RSNP.1.PS.A_homer_format_0.001.txt SOX9.H13RSNP.1.PS.A_homer_format_0.0005.txt SOX9.H13RSNP.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1561.75	1842.75	1896.75	2024.75
02	579.25	2919.25	1903.25	1924.25
03	684.0	3341.0	384.0	2917.0
04	7318.0	0.0	0.0	8.0
05	0.0	0.0	0.0	7326.0
06	0.0	0.0	0.0	7326.0
07	0.0	0.0	7326.0	0.0
08	21.0	0.0	0.0	7305.0
09	814.25	955.25	1109.25	4447.25
10	1330.5	2297.5	1313.5	2384.5

PFM

	A	C	G	T
01	0.213	0.252	0.259	0.276
02	0.079	0.398	0.26	0.263
03	0.093	0.456	0.052	0.398
04	0.999	0.0	0.0	0.001
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	1.0	0.0
08	0.003	0.0	0.0	0.997
09	0.111	0.13	0.151	0.607
10	0.182	0.314	0.179	0.325

PWM

	A	C	G	T
01	-0.159	0.006	0.035	0.1
02	-1.149	0.466	0.038	0.049
03	-0.983	0.601	-1.558	0.465
04	1.384	-6.714	-6.714	-5.189
05	-6.714	-6.714	-6.714	1.385
06	-6.714	-6.714	-6.714	1.385
07	-6.714	-6.714	1.385	-6.714
08	-4.369	-6.714	-6.714	1.383
09	-0.809	-0.65	-0.501	0.886
10	-0.319	0.226	-0.332	0.264

Standard thresholds

P-value	Threshold
0.001	2.996855
0.0005	6.011775
0.0001	7.675055