SOX30.H12INVIVO.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX30.H12INVIVO.0.P.C
Gene (human)	SOX30 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox30
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	11
Consensus	nSCWYTGTSWY
GC content	51.94%
Information content (bits; total / per base)	9.806 / 0.891
Data sources	ChIP-Seq
Aligned words	227

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
Mouse	1 (7)	0.577	0.659	0.468	0.556	0.63	0.757	2.087	3.249	10.222	12.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.748	0.677	0.695	0.641	0.634	0.604
Overall, 3 experiments	best	0.782	0.715	0.708	0.662	0.635	0.613
Methyl HT-SELEX, 1 experiments	median	0.782	0.715	0.708	0.662	0.635	0.613
Methyl HT-SELEX, 1 experiments	best	0.782	0.715	0.708	0.662	0.635	0.613
Non-Methyl HT-SELEX, 2 experiments	median	0.647	0.602	0.614	0.581	0.578	0.56
Non-Methyl HT-SELEX, 2 experiments	best	0.748	0.677	0.695	0.641	0.634	0.604

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.633	0.071	0.578	0.459

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 H {4.1.1.8} (TFClass)
TFClass ID	TFClass: 4.1.1.8.1
HGNC	HGNC:30635
MGI	MGI:1341157
EntrezGene (human)	GeneID:11063 (SSTAR profile)
EntrezGene (mouse)	GeneID:214105 (SSTAR profile)
UniProt ID (human)	SOX30_HUMAN
UniProt ID (mouse)	SOX30_MOUSE
UniProt AC (human)	O94993 (TFClass)
UniProt AC (mouse)	Q8CGW4 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	2
Methyl-HT-SELEX	1

PCM	SOX30.H12INVIVO.0.P.C.pcm
PWM	SOX30.H12INVIVO.0.P.C.pwm
PFM	SOX30.H12INVIVO.0.P.C.pfm
Alignment	SOX30.H12INVIVO.0.P.C.words.tsv
Threshold to P-value map	SOX30.H12INVIVO.0.P.C.thr
Motif in other formats
JASPAR format	SOX30.H12INVIVO.0.P.C_jaspar_format.txt
MEME format	SOX30.H12INVIVO.0.P.C_meme_format.meme
Transfac format	SOX30.H12INVIVO.0.P.C_transfac_format.txt
Homer format	SOX30.H12INVIVO.0.P.C_homer_format_0.001.txt SOX30.H12INVIVO.0.P.C_homer_format_0.0005.txt SOX30.H12INVIVO.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	40.0	56.0	44.0	87.0
02	6.0	141.0	63.0	17.0
03	6.0	199.0	14.0	8.0
04	125.0	11.0	12.0	79.0
05	1.0	98.0	3.0	125.0
06	3.0	6.0	5.0	213.0
07	8.0	27.0	187.0	5.0
08	1.0	4.0	3.0	219.0
09	14.0	28.0	169.0	16.0
10	149.0	22.0	22.0	34.0
11	5.0	148.0	35.0	39.0

PFM

	A	C	G	T
01	0.176	0.247	0.194	0.383
02	0.026	0.621	0.278	0.075
03	0.026	0.877	0.062	0.035
04	0.551	0.048	0.053	0.348
05	0.004	0.432	0.013	0.551
06	0.013	0.026	0.022	0.938
07	0.035	0.119	0.824	0.022
08	0.004	0.018	0.013	0.965
09	0.062	0.123	0.744	0.07
10	0.656	0.097	0.097	0.15
11	0.022	0.652	0.154	0.172

PWM

	A	C	G	T
01	-0.34	-0.013	-0.248	0.419
02	-2.067	0.896	0.102	-1.152
03	-2.067	1.238	-1.331	-1.826
04	0.777	-1.548	-1.47	0.324
05	-3.205	0.536	-2.591	0.777
06	-2.591	-2.067	-2.213	1.305
07	-1.826	-0.717	1.176	-2.213
08	-3.205	-2.384	-2.591	1.333
09	-1.331	-0.683	1.076	-1.208
10	0.951	-0.911	-0.911	-0.497
11	-2.213	0.944	-0.469	-0.365

Standard thresholds

P-value	Threshold
0.001	4.81502
0.0005	5.60827
0.0001	7.2004