LEF1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LEF1.H12INVIVO.0.PSM.A
Gene (human)	LEF1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Lef1
Gene synonyms (mouse)	Lef-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	bbCTTTGATSYbb
GC content	43.67%
Information content (bits; total / per base)	12.367 / 0.951
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1002

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	5 (27)	0.729	0.941	0.589	0.91	0.717	0.938	2.029	4.487	39.721	231.119
Mouse	3 (19)	0.747	0.951	0.687	0.919	0.748	0.945	2.647	4.566	76.056	395.161

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.917	0.905	0.753	0.774	0.604	0.653
Overall, 6 experiments	best	0.996	0.994	0.934	0.934	0.809	0.795
Methyl HT-SELEX, 2 experiments	median	0.994	0.99	0.884	0.893	0.681	0.734
Methyl HT-SELEX, 2 experiments	best	0.996	0.994	0.934	0.934	0.722	0.769
Non-Methyl HT-SELEX, 4 experiments	median	0.707	0.71	0.595	0.613	0.539	0.562
Non-Methyl HT-SELEX, 4 experiments	best	0.969	0.954	0.913	0.89	0.809	0.795

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.613	0.333	0.551	0.326

TF superclass	Other all-alpha-helical DNA-binding domains {4} (TFClass)
TF class	High-mobility group (HMG) domain factors {4.1} (TFClass)
TF family	TCF7-related {4.1.3} (TFClass)
TF subfamily	{4.1.3.0} (TFClass)
TFClass ID	TFClass: 4.1.3.0.4
HGNC	HGNC:6551
MGI	MGI:96770
EntrezGene (human)	GeneID:51176 (SSTAR profile)
EntrezGene (mouse)	GeneID:16842 (SSTAR profile)
UniProt ID (human)	LEF1_HUMAN
UniProt ID (mouse)	LEF1_MOUSE
UniProt AC (human)	Q9UJU2 (TFClass)
UniProt AC (mouse)	P27782 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 3 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	LEF1.H12INVIVO.0.PSM.A.pcm
PWM	LEF1.H12INVIVO.0.PSM.A.pwm
PFM	LEF1.H12INVIVO.0.PSM.A.pfm
Alignment	LEF1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	LEF1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	LEF1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	LEF1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	LEF1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	LEF1.H12INVIVO.0.PSM.A_homer_format_0.001.txt LEF1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt LEF1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	92.0	298.0	310.0	302.0
02	74.0	509.0	218.0	201.0
03	18.0	851.0	45.0	88.0
04	16.0	18.0	1.0	967.0
05	5.0	54.0	19.0	924.0
06	18.0	3.0	6.0	975.0
07	12.0	141.0	819.0	30.0
08	894.0	34.0	9.0	65.0
09	209.0	6.0	13.0	774.0
10	17.0	406.0	572.0	7.0
11	73.0	140.0	13.0	776.0
12	77.0	215.0	403.0	307.0
13	141.0	194.0	392.0	275.0

PFM

	A	C	G	T
01	0.092	0.297	0.309	0.301
02	0.074	0.508	0.218	0.201
03	0.018	0.849	0.045	0.088
04	0.016	0.018	0.001	0.965
05	0.005	0.054	0.019	0.922
06	0.018	0.003	0.006	0.973
07	0.012	0.141	0.817	0.03
08	0.892	0.034	0.009	0.065
09	0.209	0.006	0.013	0.772
10	0.017	0.405	0.571	0.007
11	0.073	0.14	0.013	0.774
12	0.077	0.215	0.402	0.306
13	0.141	0.194	0.391	0.274

PWM

	A	C	G	T
01	-0.99	0.173	0.212	0.186
02	-1.203	0.706	-0.138	-0.218
03	-2.548	1.218	-1.686	-1.034
04	-2.655	-2.548	-4.527	1.346
05	-3.624	-1.51	-2.499	1.3
06	-2.548	-3.977	-3.486	1.354
07	-2.911	-0.569	1.18	-2.073
08	1.267	-1.954	-3.158	-1.33
09	-0.18	-3.486	-2.841	1.123
10	-2.6	0.48	0.822	-3.364
11	-1.216	-0.576	-2.841	1.126
12	-1.164	-0.152	0.473	0.202
13	-0.569	-0.254	0.445	0.093

Standard thresholds

P-value	Threshold
0.001	4.016915
0.0005	5.037965
0.0001	7.133915