FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map

Table 1 Number of inferred promoter models obtained by four alternative methods on the ENCODE DHS dataset

Method type	Number of promoter models	Number of E–P links	Number of unique enhancers
Pairwise (r ≥ 0.7)+ FDR	39,372	139,170	53,950
OLS-LASSO (R² ≥ 0.5)^a	39,368	122,064	74,104
OLS-enet (R² ≥ 0.5)^a	39,407	150,158	85,926
FOCS	70,465	167,988	92,603

^aThe number of OLS models (R² ≥ 0.5) was 39,892 before LASSO/enet shrinkage. These methods eliminate models in which no enhancer passed the shrinkage

ISSN: 1474-760X