SNAI1.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SNAI1.H12RSNP.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	dRCAGGTGb
GC content	64.37%
Information content (bits; total / per base)	12.09 / 1.343
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	997

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)	0.529	0.758	0.406	0.718	0.41	0.735	0.911	2.646	4.699	218.959
Mouse	8 (55)	0.905	0.955	0.831	0.909	0.899	0.946	3.315	3.78	179.268	276.638

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.943	0.931	0.861	0.855	0.8	0.801
Overall, 4 experiments	best	0.998	0.997	0.995	0.993	0.991	0.986
Methyl HT-SELEX, 2 experiments	median	0.943	0.931	0.864	0.861	0.811	0.814
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.995	0.993	0.991	0.986
Non-Methyl HT-SELEX, 2 experiments	median	0.943	0.931	0.857	0.855	0.797	0.8
Non-Methyl HT-SELEX, 2 experiments	best	0.992	0.987	0.989	0.982	0.969	0.96

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.983	0.8	0.959	0.581

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.H12RSNP.0.PSM.A.pcm
PWM	SNAI1.H12RSNP.0.PSM.A.pwm
PFM	SNAI1.H12RSNP.0.PSM.A.pfm
Alignment	SNAI1.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	SNAI1.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	SNAI1.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	SNAI1.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	SNAI1.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	SNAI1.H12RSNP.0.PSM.A_homer_format_0.001.txt SNAI1.H12RSNP.0.PSM.A_homer_format_0.0005.txt SNAI1.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	489.0	65.0	326.0	117.0
02	250.0	10.0	707.0	30.0
03	17.0	964.0	8.0	8.0
04	977.0	5.0	6.0	9.0
05	18.0	8.0	961.0	10.0
06	7.0	12.0	973.0	5.0
07	20.0	7.0	7.0	963.0
08	6.0	15.0	940.0	36.0
09	29.0	496.0	266.0	206.0

PFM

	A	C	G	T
01	0.49	0.065	0.327	0.117
02	0.251	0.01	0.709	0.03
03	0.017	0.967	0.008	0.008
04	0.98	0.005	0.006	0.009
05	0.018	0.008	0.964	0.01
06	0.007	0.012	0.976	0.005
07	0.02	0.007	0.007	0.966
08	0.006	0.015	0.943	0.036
09	0.029	0.497	0.267	0.207

PWM

	A	C	G	T
01	0.671	-1.325	0.267	-0.749
02	0.003	-3.064	1.038	-2.068
03	-2.595	1.348	-3.251	-3.251
04	1.361	-3.619	-3.481	-3.153
05	-2.543	-3.251	1.344	-3.064
06	-3.359	-2.906	1.357	-3.619
07	-2.447	-3.359	-3.359	1.346
08	-3.481	-2.708	1.322	-1.895
09	-2.1	0.685	0.065	-0.189

Standard thresholds

P-value	Threshold
0.001	4.152565
0.0005	5.09048
0.0001	6.92125