Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes.

ABSTRACT: Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that genetic correlation due to linkage disequilibrium confounds fine-mapping in genome-wide association studies (GWAS). We developed a non-parametric permutation-based procedure to establish stringent statistical criteria to control the risk of false-positive associations in enhancer-gene association studies (EGAS). We applied our procedure to large-scale transcriptome and epigenome data from multiple tissues and species, including the mouse and human brain, to predict enhancer-gene associations genome wide. We tested the functional validity of our prediction

SUBMITTER: Xie F 

PROVIDER: S-EPMC10363915 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature