Additional file 2 of Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data

Additional file 2: Table S1: Overview of the top 19 EnTDefs, including the ranks, enhancer/enhancer-gene link methods, and basic summary statistics. Table S2: The 31 ENCODE ChIP-seq datasets from 9 completely different cell lines and 14 completely different transcription factors. Table S3: The nine ChIA-PET datasets used for generating cell-type-specific EnTDefs (CT-EnTDefs) and number of TFs assayed by ENCODE ChIP-seq in each particular cell type, which were used to evaluate the performance of the CT-EnTDefs. Table S4: Overview of the seven independent datasets used for the comparative analysis. Table S5: ChIA-PET datasets used by “ChIA” and “Loop” methods to assign enhancer to target genes in a cell-type independent manner (general EnTDefs). Table S6: The 87 ENCODE ChIP-seq datasets used for EnTDef evaluation (evaluation ChIP-seq) (tab 1) and the TF vs. cell type matrix (tab 2). Table S7: The 13 ENCODE ChIP-seq datasets from 4 different cell lines (testing ChIP-seq).