SCRT1.H13RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SCRT1.H13RSNP.0.PSM.A
Gene (human)	SCRT1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Scrt1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	hGCAACAGGTGn
GC content	54.04%
Information content (bits; total / per base)	19.331 / 1.611
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	364
Previous names	SCRT1.H12RSNP.0.PSM.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	2 (12)	0.604	0.743	0.545	0.735	0.918	0.969	4.19	5.366	280.678	772.42

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.838	0.846	0.793	0.8	0.775	0.779
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.999	0.999	0.996	0.996
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.999	0.999	0.996	0.996
Non-Methyl HT-SELEX, 3 experiments	median	0.677	0.693	0.586	0.601	0.553	0.562
Non-Methyl HT-SELEX, 3 experiments	best	1.0	1.0	1.0	1.0	0.999	0.999

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.991	0.773	0.958	0.598
batch 2	0.916	0.853	0.918	0.693

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	More than 3 adjacent zinc fingers {2.3.3} (TFClass)
TF subfamily	Snail-like {2.3.3.2} (TFClass)
TFClass ID	TFClass: 2.3.3.2.4
HGNC	HGNC:15950
MGI	MGI:2176606
EntrezGene (human)	GeneID:83482 (SSTAR profile)
EntrezGene (mouse)	GeneID:170729 (SSTAR profile)
UniProt ID (human)	SCRT1_HUMAN
UniProt ID (mouse)	SCRT1_MOUSE
UniProt AC (human)	Q9BWW7 (TFClass)
UniProt AC (mouse)	Q99M85 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SCRT1.H13RSNP.0.PSM.A.pcm
PWM	SCRT1.H13RSNP.0.PSM.A.pwm
PFM	SCRT1.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	SCRT1.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	SCRT1.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	SCRT1.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	SCRT1.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	SCRT1.H13RSNP.0.PSM.A_homer_format_0.001.txt SCRT1.H13RSNP.0.PSM.A_homer_format_0.0005.txt SCRT1.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	136.75	49.75	42.75	134.75
02	0.0	0.0	243.0	121.0
03	0.0	364.0	0.0	0.0
04	364.0	0.0	0.0	0.0
05	364.0	0.0	0.0	0.0
06	0.0	364.0	0.0	0.0
07	364.0	0.0	0.0	0.0
08	0.0	0.0	364.0	0.0
09	0.0	0.0	364.0	0.0
10	0.0	0.0	0.0	364.0
11	0.0	0.0	364.0	0.0
12	59.0	74.0	131.0	100.0

PFM

	A	C	G	T
01	0.376	0.137	0.117	0.37
02	0.0	0.0	0.668	0.332
03	0.0	1.0	0.0	0.0
04	1.0	0.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	1.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	1.0	0.0
09	0.0	0.0	1.0	0.0
10	0.0	0.0	0.0	1.0
11	0.0	0.0	1.0	0.0
12	0.162	0.203	0.36	0.275

PWM

	A	C	G	T
01	0.402	-0.591	-0.738	0.387
02	-4.139	-4.139	0.972	0.281
03	-4.139	1.374	-4.139	-4.139
04	1.374	-4.139	-4.139	-4.139
05	1.374	-4.139	-4.139	-4.139
06	-4.139	1.374	-4.139	-4.139
07	1.374	-4.139	-4.139	-4.139
08	-4.139	-4.139	1.374	-4.139
09	-4.139	-4.139	1.374	-4.139
10	-4.139	-4.139	-4.139	1.374
11	-4.139	-4.139	1.374	-4.139
12	-0.425	-0.203	0.359	0.093

Standard thresholds

P-value	Threshold
0.001	-2.437125
0.0005	1.46491
0.0001	2.996875