SNAI1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SNAI1.H12INVITRO.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	12
Consensus	ndRCAGGTGYdn
GC content	57.89%
Information content (bits; total / per base)	13.561 / 1.13
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	5494

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)	0.521	0.772	0.39	0.715	0.399	0.732	0.912	2.675	4.367	220.658
Mouse	8 (55)	0.885	0.937	0.821	0.911	0.892	0.941	3.519	4.239	180.027	277.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.946	0.938	0.861	0.86	0.8	0.803
Overall, 4 experiments	best	0.998	0.996	0.996	0.993	0.993	0.989
Methyl HT-SELEX, 2 experiments	median	0.946	0.937	0.863	0.863	0.812	0.817
Methyl HT-SELEX, 2 experiments	best	0.998	0.996	0.996	0.993	0.993	0.989
Non-Methyl HT-SELEX, 2 experiments	median	0.946	0.938	0.861	0.86	0.797	0.803
Non-Methyl HT-SELEX, 2 experiments	best	0.994	0.989	0.991	0.984	0.968	0.96

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.98	0.793	0.952	0.589

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.H12INVITRO.0.PSM.A.pcm
PWM	SNAI1.H12INVITRO.0.PSM.A.pwm
PFM	SNAI1.H12INVITRO.0.PSM.A.pfm
Alignment	SNAI1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SNAI1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SNAI1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SNAI1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SNAI1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SNAI1.H12INVITRO.0.PSM.A_homer_format_0.001.txt SNAI1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SNAI1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1044.25	1165.25	1683.25	1601.25
02	2339.5	533.5	1682.5	938.5
03	2160.0	15.0	3148.0	171.0
04	76.0	5321.0	96.0	1.0
05	5494.0	0.0	0.0	0.0
06	0.0	0.0	5494.0	0.0
07	0.0	0.0	5494.0	0.0
08	0.0	0.0	0.0	5494.0
09	2.0	0.0	5492.0	0.0
10	185.0	3075.0	815.0	1419.0
11	2923.25	627.25	1021.25	922.25
12	1235.75	1380.75	1123.75	1753.75

PFM

	A	C	G	T
01	0.19	0.212	0.306	0.291
02	0.426	0.097	0.306	0.171
03	0.393	0.003	0.573	0.031
04	0.014	0.969	0.017	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	1.0	0.0
10	0.034	0.56	0.148	0.258
11	0.532	0.114	0.186	0.168
12	0.225	0.251	0.205	0.319

PWM

	A	C	G	T
01	-0.274	-0.164	0.203	0.153
02	0.532	-0.943	0.203	-0.38
03	0.452	-4.385	0.829	-2.073
04	-2.868	1.353	-2.64	-6.078
05	1.385	-6.46	-6.46	-6.46
06	-6.46	-6.46	1.385	-6.46
07	-6.46	-6.46	1.385	-6.46
08	-6.46	-6.46	-6.46	1.385
09	-5.803	-6.46	1.385	-6.46
10	-1.995	0.805	-0.521	0.033
11	0.755	-0.782	-0.296	-0.398
12	-0.106	0.005	-0.2	0.244

Standard thresholds

P-value	Threshold
0.001	1.403185
0.0005	2.718825
0.0001	7.1105