Fig. 3

Evaluation of cell-type-specific (CT)-EnTDefs and general EnTDefs. A Distribution of the average F1 scores of same-CT EnTDefs, diff-CT EnTDefs, and general EnTDefs that were applied on the same TF ChIP-seq data. B Correlation between average F1 scores calculated on a TF in a particular cell type using CT-EnTDefs of the matched cell type (“same-CT.EnTDef” on the x-axis) and the ones calculated on the same TF using CT-EnTDefs of a different cell type (“diff-CT.EnTDef” on the y-axis). Each dot represents an average F1 score of a TF across the top 10 EnTDefs, and each panel is one of four cell types (GM12878, H1HESC, K562, and MCF7) for which the CT-EnTDefs were created and evaluated, respectively. C Evaluation summary of different types of EnTDefs (i.e., same-CT EnTDefs, diff-CT EnTDefs, and general EnTDefs) in four different cell types. Comparative average F1 scores associated with the TF ChIP-seq datasets of a particular cell type are grouped in a grey dashed box: blue refers to using the CT-EnTDef of the same cell type (same-CT.EnTDef), green refers to using the general CT-EnTDef excluding the enhancer-gene pairs from that cell type, and red refers to using the CT-EnTDef of a different cell type (diff-CT.EnTDef)