SNAI1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SNAI1.H12INVIVO.0.PSM.A
Gene (human)	SNAI1 (GeneCards)
Gene synonyms (human)	SNAH
Gene (mouse)	Snai1
Gene synonyms (mouse)	Sna
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	RGCAGGTGS
GC content	64.89%
Information content (bits; total / per base)	13.284 / 1.476
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	281

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	1 (5)	0.535	0.761	0.404	0.718	0.403	0.731	0.89	2.623	4.745	214.268
Mouse	8 (55)	0.907	0.959	0.836	0.913	0.898	0.948	3.318	3.819	183.086	293.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.944	0.933	0.856	0.855	0.796	0.8
Overall, 4 experiments	best	0.997	0.996	0.996	0.993	0.991	0.987
Methyl HT-SELEX, 2 experiments	median	0.943	0.932	0.857	0.858	0.805	0.812
Methyl HT-SELEX, 2 experiments	best	0.997	0.996	0.996	0.993	0.991	0.987
Non-Methyl HT-SELEX, 2 experiments	median	0.944	0.933	0.856	0.855	0.796	0.8
Non-Methyl HT-SELEX, 2 experiments	best	0.992	0.987	0.989	0.982	0.97	0.961

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.977	0.788	0.956	0.574

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: 2.3.3.2.1
HGNC	HGNC:11128
MGI	MGI:98330
EntrezGene (human)	GeneID:6615 (SSTAR profile)
EntrezGene (mouse)	GeneID:20613 (SSTAR profile)
UniProt ID (human)	SNAI1_HUMAN
UniProt ID (mouse)	SNAI1_MOUSE
UniProt AC (human)	O95863 (TFClass)
UniProt AC (mouse)	Q02085 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 8 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SNAI1.H12INVIVO.0.PSM.A.pcm
PWM	SNAI1.H12INVIVO.0.PSM.A.pwm
PFM	SNAI1.H12INVIVO.0.PSM.A.pfm
Alignment	SNAI1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SNAI1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SNAI1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SNAI1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SNAI1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SNAI1.H12INVIVO.0.PSM.A_homer_format_0.001.txt SNAI1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SNAI1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	158.0	14.0	84.0	25.0
02	70.0	1.0	205.0	5.0
03	1.0	280.0	0.0	0.0
04	278.0	1.0	1.0	1.0
05	5.0	1.0	273.0	2.0
06	0.0	3.0	278.0	0.0
07	2.0	2.0	0.0	277.0
08	1.0	1.0	275.0	4.0
09	12.0	173.0	49.0	47.0

PFM

	A	C	G	T
01	0.562	0.05	0.299	0.089
02	0.249	0.004	0.73	0.018
03	0.004	0.996	0.0	0.0
04	0.989	0.004	0.004	0.004
05	0.018	0.004	0.972	0.007
06	0.0	0.011	0.989	0.0
07	0.007	0.007	0.0	0.986
08	0.004	0.004	0.979	0.014
09	0.043	0.616	0.174	0.167

PWM

	A	C	G	T
01	0.8	-1.537	0.176	-0.998
02	-0.003	-3.392	1.058	-2.414
03	-3.392	1.368	-3.929	-3.929
04	1.361	-3.392	-3.392	-3.392
05	-2.414	-3.392	1.343	-3.045
06	-3.929	-2.788	1.361	-3.929
07	-3.045	-3.045	-3.929	1.357
08	-3.392	-3.392	1.35	-2.584
09	-1.676	0.889	-0.352	-0.392

Standard thresholds

P-value	Threshold
0.001	3.781085
0.0005	4.836265
0.0001	6.79663