SNAI2.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SNAI2.H12INVIVO.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	11
Consensus	dRCAGGTGYnb
GC content	61.4%
Information content (bits; total / per base)	13.888 / 1.263
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	996

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)	0.916	0.967	0.816	0.901	0.923	0.976	3.727	4.333	218.367	709.796

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.997	0.994	0.994	0.99	0.99	0.985
Overall, 5 experiments	best	0.999	0.997	0.997	0.995	0.995	0.992
Methyl HT-SELEX, 2 experiments	median	0.996	0.993	0.989	0.984	0.908	0.916
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.997	0.994	0.995	0.992
Non-Methyl HT-SELEX, 3 experiments	median	0.997	0.994	0.994	0.99	0.99	0.985
Non-Methyl HT-SELEX, 3 experiments	best	0.999	0.997	0.997	0.995	0.995	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.36	13.988	0.161	0.278

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.988	0.862	0.956	0.557

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.H12INVIVO.0.PSM.A.pcm
PWM	SNAI2.H12INVIVO.0.PSM.A.pwm
PFM	SNAI2.H12INVIVO.0.PSM.A.pfm
Alignment	SNAI2.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SNAI2.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SNAI2.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SNAI2.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SNAI2.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SNAI2.H12INVIVO.0.PSM.A_homer_format_0.001.txt SNAI2.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SNAI2.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	418.0	49.0	426.0	103.0
02	440.0	0.0	550.0	6.0
03	0.0	995.0	0.0	1.0
04	995.0	0.0	1.0	0.0
05	6.0	0.0	990.0	0.0
06	1.0	0.0	995.0	0.0
07	1.0	1.0	0.0	994.0
08	1.0	0.0	992.0	3.0
09	27.0	594.0	165.0	210.0
10	381.0	234.0	192.0	189.0
11	111.0	234.0	309.0	342.0

PFM

	A	C	G	T
01	0.42	0.049	0.428	0.103
02	0.442	0.0	0.552	0.006
03	0.0	0.999	0.0	0.001
04	0.999	0.0	0.001	0.0
05	0.006	0.0	0.994	0.0
06	0.001	0.0	0.999	0.0
07	0.001	0.001	0.0	0.998
08	0.001	0.0	0.996	0.003
09	0.027	0.596	0.166	0.211
10	0.383	0.235	0.193	0.19
11	0.111	0.235	0.31	0.343

PWM

	A	C	G	T
01	0.515	-1.598	0.534	-0.873
02	0.566	-4.979	0.789	-3.48
03	-4.979	1.38	-4.979	-4.522
04	1.38	-4.979	-4.522	-4.979
05	-3.48	-4.979	1.375	-4.979
06	-4.522	-4.979	1.38	-4.979
07	-4.522	-4.522	-4.979	1.379
08	-4.522	-4.979	1.377	-3.971
09	-2.167	0.865	-0.408	-0.169
10	0.423	-0.062	-0.258	-0.274
11	-0.799	-0.062	0.215	0.315

Standard thresholds

P-value	Threshold
0.001	2.617935
0.0005	3.575805
0.0001	6.710075