SNAI2.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SNAI2.H12RSNP.0.PSM.A
Gene (human)	SNAI2 (GeneCards)
Gene synonyms (human)	SLUG, SLUGH
Gene (mouse)	Snai2
Gene synonyms (mouse)	Slug, Slugh
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	RGCAGGTGb
GC content	65.86%
Information content (bits; total / per base)	13.678 / 1.52
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	152

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	14 (76)	0.895	0.954	0.788	0.875	0.912	0.968	3.246	3.813	205.585	695.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.992	0.987	0.991	0.984	0.991	0.983
Overall, 5 experiments	best	0.995	0.993	0.994	0.99	0.994	0.989
Methyl HT-SELEX, 2 experiments	median	0.991	0.987	0.986	0.978	0.908	0.913
Methyl HT-SELEX, 2 experiments	best	0.995	0.992	0.994	0.99	0.994	0.989
Non-Methyl HT-SELEX, 3 experiments	median	0.992	0.987	0.991	0.984	0.991	0.983
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.993	0.994	0.989	0.993	0.988

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.689	15.764	0.165	0.261

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.988	0.872	0.961	0.546

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: 2.3.3.2.2
HGNC	HGNC:11094
MGI	MGI:1096393
EntrezGene (human)	GeneID:6591 (SSTAR profile)
EntrezGene (mouse)	GeneID:20583 (SSTAR profile)
UniProt ID (human)	SNAI2_HUMAN
UniProt ID (mouse)	SNAI2_MOUSE
UniProt AC (human)	O43623 (TFClass)
UniProt AC (mouse)	P97469 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	14 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	SNAI2.H12RSNP.0.PSM.A.pcm
PWM	SNAI2.H12RSNP.0.PSM.A.pwm
PFM	SNAI2.H12RSNP.0.PSM.A.pfm
Alignment	SNAI2.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	SNAI2.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	SNAI2.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	SNAI2.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	SNAI2.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	SNAI2.H12RSNP.0.PSM.A_homer_format_0.001.txt SNAI2.H12RSNP.0.PSM.A_homer_format_0.0005.txt SNAI2.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	46.0	7.0	81.0	18.0
02	46.0	0.0	106.0	0.0
03	0.0	152.0	0.0	0.0
04	152.0	0.0	0.0	0.0
05	0.0	0.0	152.0	0.0
06	0.0	0.0	152.0	0.0
07	0.0	0.0	0.0	152.0
08	0.0	0.0	152.0	0.0
09	15.0	60.0	39.0	38.0

PFM

	A	C	G	T
01	0.303	0.046	0.533	0.118
02	0.303	0.0	0.697	0.0
03	0.0	1.0	0.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.099	0.395	0.257	0.25

PWM

	A	C	G	T
01	0.185	-1.559	0.74	-0.712
02	0.185	-3.442	1.005	-3.442
03	-3.442	1.362	-3.442	-3.442
04	1.362	-3.442	-3.442	-3.442
05	-3.442	-3.442	1.362	-3.442
06	-3.442	-3.442	1.362	-3.442
07	-3.442	-3.442	-3.442	1.362
08	-3.442	-3.442	1.362	-3.442
09	-0.882	0.445	0.025	0.0

Standard thresholds

P-value	Threshold
0.001	4.081995
0.0005	4.680065
0.0001	7.07209