SOX30.H13RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX30.H13RSNP.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	11
Consensus	nSYATTGTThn
GC content	40.06%
Information content (bits; total / per base)	12.519 / 1.138
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	5913
Previous names	SOX30.H12RSNP.1.SM.B

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)	0.509	0.563	0.36	0.401	0.514	0.66	1.242	1.801	0.086	2.469

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.938	0.909	0.844	0.819	0.701	0.709
Overall, 3 experiments	best	0.951	0.928	0.856	0.835	0.713	0.721
Methyl HT-SELEX, 1 experiments	median	0.951	0.928	0.856	0.835	0.713	0.721
Methyl HT-SELEX, 1 experiments	best	0.951	0.928	0.856	0.835	0.713	0.721
Non-Methyl HT-SELEX, 2 experiments	median	0.826	0.79	0.734	0.713	0.635	0.638
Non-Methyl HT-SELEX, 2 experiments	best	0.938	0.909	0.844	0.819	0.701	0.709

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.819	0.231	0.804	0.617

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

PCM	SOX30.H13RSNP.1.SM.B.pcm
PWM	SOX30.H13RSNP.1.SM.B.pwm
PFM	SOX30.H13RSNP.1.SM.B.pfm
Threshold to P-value map	SOX30.H13RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	SOX30.H13RSNP.1.SM.B_jaspar_format.txt
MEME format	SOX30.H13RSNP.1.SM.B_meme_format.meme
Transfac format	SOX30.H13RSNP.1.SM.B_transfac_format.txt
Homer format	SOX30.H13RSNP.1.SM.B_homer_format_0.001.txt SOX30.H13RSNP.1.SM.B_homer_format_0.0005.txt SOX30.H13RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1260.75	1426.75	1476.75	1748.75
02	193.5	3251.5	1288.5	1179.5
03	478.0	3943.0	635.0	857.0
04	5913.0	0.0	0.0	0.0
05	0.0	0.0	0.0	5913.0
06	0.0	0.0	0.0	5913.0
07	0.0	0.0	5913.0	0.0
08	0.0	0.0	0.0	5913.0
09	21.0	1151.0	49.0	4692.0
10	820.25	3262.25	760.25	1070.25
11	1109.25	1467.25	1429.25	1907.25

PFM

	A	C	G	T
01	0.213	0.241	0.25	0.296
02	0.033	0.55	0.218	0.199
03	0.081	0.667	0.107	0.145
04	1.0	0.0	0.0	0.0
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	0.0	0.0	0.0	1.0
09	0.004	0.195	0.008	0.794
10	0.139	0.552	0.129	0.181
11	0.188	0.248	0.242	0.323

PWM

	A	C	G	T
01	-0.159	-0.035	-0.001	0.168
02	-2.024	0.787	-0.137	-0.225
03	-1.126	0.98	-0.843	-0.544
04	1.385	-6.525	-6.525	-6.525
05	-6.525	-6.525	-6.525	1.385
06	-6.525	-6.525	-6.525	1.385
07	-6.525	-6.525	1.385	-6.525
08	-6.525	-6.525	-6.525	1.385
09	-4.157	-0.25	-3.365	1.154
10	-0.588	0.791	-0.664	-0.322
11	-0.287	-0.007	-0.034	0.254

Standard thresholds

P-value	Threshold
0.001	1.572625
0.0005	4.086265
0.0001	7.77273