LEF1.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	LEF1.H12CORE.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	12
Consensus	bbCTTTGATSYn
GC content	40.08%
Information content (bits; total / per base)	13.995 / 1.166
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2419

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)	0.701	0.914	0.545	0.885	0.666	0.898	1.789	3.994	39.469	209.284
Mouse	3 (19)	0.713	0.908	0.662	0.851	0.686	0.894	2.383	3.818	76.167	381.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.927	0.917	0.761	0.781	0.612	0.659
Overall, 6 experiments	best	0.997	0.996	0.939	0.938	0.829	0.816
Methyl HT-SELEX, 2 experiments	median	0.995	0.992	0.891	0.898	0.691	0.74
Methyl HT-SELEX, 2 experiments	best	0.997	0.996	0.939	0.938	0.732	0.775
Non-Methyl HT-SELEX, 4 experiments	median	0.708	0.714	0.596	0.615	0.54	0.564
Non-Methyl HT-SELEX, 4 experiments	best	0.977	0.965	0.929	0.91	0.829	0.816

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.646	0.364	0.598	0.379

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.H12CORE.0.PSM.A.pcm
PWM	LEF1.H12CORE.0.PSM.A.pwm
PFM	LEF1.H12CORE.0.PSM.A.pfm
Alignment	LEF1.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	LEF1.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	LEF1.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	LEF1.H12CORE.0.PSM.A_meme_format.meme
Transfac format	LEF1.H12CORE.0.PSM.A_transfac_format.txt
Homer format	LEF1.H12CORE.0.PSM.A_homer_format_0.001.txt LEF1.H12CORE.0.PSM.A_homer_format_0.0005.txt LEF1.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	335.5	896.5	469.5	717.5
02	306.5	1098.5	562.5	451.5
03	23.0	2013.0	237.0	146.0
04	30.0	25.0	5.0	2359.0
05	1.0	1.0	0.0	2417.0
06	1.0	0.0	1.0	2417.0
07	0.0	14.0	2403.0	2.0
08	2414.0	1.0	0.0	4.0
09	179.0	9.0	9.0	2222.0
10	59.0	1322.0	1010.0	28.0
11	307.25	381.25	204.25	1526.25
12	490.25	524.25	448.25	956.25

PFM

	A	C	G	T
01	0.139	0.371	0.194	0.297
02	0.127	0.454	0.233	0.187
03	0.01	0.832	0.098	0.06
04	0.012	0.01	0.002	0.975
05	0.0	0.0	0.0	0.999
06	0.0	0.0	0.0	0.999
07	0.0	0.006	0.993	0.001
08	0.998	0.0	0.0	0.002
09	0.074	0.004	0.004	0.919
10	0.024	0.547	0.418	0.012
11	0.127	0.158	0.084	0.631
12	0.203	0.217	0.185	0.395

PWM

	A	C	G	T
01	-0.587	0.393	-0.252	0.17
02	-0.676	0.595	-0.072	-0.291
03	-3.191	1.2	-0.932	-1.411
04	-2.944	-3.114	-4.47	1.359
05	-5.327	-5.327	-5.741	1.383
06	-5.327	-5.741	-5.327	1.383
07	-5.741	-3.639	1.377	-5.035
08	1.382	-5.327	-5.741	-4.625
09	-1.21	-4.015	-4.015	1.299
10	-2.298	0.78	0.512	-3.009
11	-0.674	-0.459	-1.079	0.924
12	-0.209	-0.142	-0.298	0.457

Standard thresholds

P-value	Threshold
0.001	2.390365
0.0005	3.796445
0.0001	6.768725