Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions

Elisa Salviato, Vera Djordjilović, Judith M. Hariprakash, Ilario Tagliaferri, Koustav Pal, Francesco Ferrari
doi: https://doi.org/10.1101/2021.03.01.432687

The following table provide the complete list of candidate enhancer-target pairs (ETG) inferred in Salviato et al. The schematic workflow of our methodological framework is available at Figure 1 of the paper. The source code of the method is available in the 3D-ETG github repository.

Each line corresponds to an ETG pair, where:

  • chr, start, end: enhancer region (hg19). Promoter proximal elements are not considered (3.5 kb upstream and 1.5 kb downstream of coding and non-coding TSS).
  • symbol: target-gene symbol of protein coding genes, based on RefSeq annotations in UCSC. Target genes with overlapping promoter regions are merged as a single pairs (separated by semicolon).
  • distance: distance between mid-points of gene promoter and enhancer regions. Promoters are defined as 1.5kb upstream and 0.5kb downstream regions of TSS of coding genes.
  • cca: first canonical correlation coefficient. It is based on the enrichment of DNase-seq and H3K27ac for enhancers and DNase-seq, H3K27ac and H3K4me3 for promoters.
  • HC: Hierarchical Contact (HC) score. HC score is proportional to the likelihood of enhancer-promoter pairs co-localization within hierarchy of TADs across multiple Hi-C matrices.
  • Pval.raw: -log10 p-value obtained by testing the canonical correlation coefficient. It quantifies the amount of evidence provided by the data for the presence of synchronized activity between the enhancer and promoter gene.
  • Pval.adapt: -log10 adjusted p-values by considering the 3D co-localization information encoded in the HC score.
  • GTEx, PancanQTL, pcHiC: 1 if supported by the Genotype-Tissue Expression project, the pan-cancer eQTL analysis, or capture Hi-C experiments, respectively.

For more details, please refer to the Materials and methods section of the paper.

Clean up all the preset filters to obtained the complete list of ETG interactions.