SOX30.H12INVIVO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX30.H12INVIVO.1.SM.B
Gene (human)	SOX30 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox30
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	10
Consensus	nbSATTGTYn
GC content	40.95%
Information content (bits; total / per base)	10.984 / 1.098
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8834

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)	0.487	0.56	0.369	0.424	0.539	0.652	1.312	1.85	1.347	5.013

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.94	0.914	0.845	0.822	0.703	0.711
Overall, 3 experiments	best	0.958	0.94	0.857	0.841	0.714	0.724
Methyl HT-SELEX, 1 experiments	median	0.958	0.94	0.857	0.841	0.714	0.724
Methyl HT-SELEX, 1 experiments	best	0.958	0.94	0.857	0.841	0.714	0.724
Non-Methyl HT-SELEX, 2 experiments	median	0.82	0.784	0.731	0.71	0.634	0.636
Non-Methyl HT-SELEX, 2 experiments	best	0.94	0.914	0.845	0.822	0.703	0.711

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.788	0.206	0.802	0.554

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.1.SM.B.pcm
PWM	SOX30.H12INVIVO.1.SM.B.pwm
PFM	SOX30.H12INVIVO.1.SM.B.pfm
Alignment	SOX30.H12INVIVO.1.SM.B.words.tsv
Threshold to P-value map	SOX30.H12INVIVO.1.SM.B.thr
Motif in other formats
JASPAR format	SOX30.H12INVIVO.1.SM.B_jaspar_format.txt
MEME format	SOX30.H12INVIVO.1.SM.B_meme_format.meme
Transfac format	SOX30.H12INVIVO.1.SM.B_transfac_format.txt
Homer format	SOX30.H12INVIVO.1.SM.B_homer_format_0.001.txt SOX30.H12INVIVO.1.SM.B_homer_format_0.0005.txt SOX30.H12INVIVO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1795.25	2209.25	2547.25	2282.25
02	377.5	4420.5	2331.5	1704.5
03	679.0	5283.0	1662.0	1210.0
04	8638.0	14.0	13.0	169.0
05	0.0	3.0	0.0	8831.0
06	0.0	3.0	0.0	8831.0
07	17.0	18.0	8799.0	0.0
08	4.0	23.0	4.0	8803.0
09	465.25	2931.25	912.25	4525.25
10	1703.75	3195.75	1803.75	2130.75

PFM

	A	C	G	T
01	0.203	0.25	0.288	0.258
02	0.043	0.5	0.264	0.193
03	0.077	0.598	0.188	0.137
04	0.978	0.002	0.001	0.019
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.002	0.002	0.996	0.0
08	0.0	0.003	0.0	0.996
09	0.053	0.332	0.103	0.512
10	0.193	0.362	0.204	0.241

PWM

	A	C	G	T
01	-0.207	0.0	0.143	0.033
02	-1.762	0.693	0.054	-0.259
03	-1.177	0.872	-0.284	-0.601
04	1.363	-4.912	-4.975	-2.558
05	-6.881	-6.039	-6.881	1.385
06	-6.881	-6.039	-6.881	1.385
07	-4.742	-4.692	1.382	-6.881
08	-5.865	-4.471	-5.865	1.382
09	-1.554	0.283	-0.883	0.717
10	-0.259	0.369	-0.202	-0.036

Standard thresholds

P-value	Threshold
0.001	3.82533
0.0005	5.876715
0.0001	7.80657