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

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

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
  1. 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