GRAIGH: Gene Regulation accessibility integrating GeneHancer database

Abstract

Single-cell assays for transposase-accessible chromatin sequencing data represent a potent tool for exploring the epigenetic heterogeneity within cell populations. Despite their power, understanding the chromatin accessibility landscape poses challenges. This study introduces Gene Regulation Accessibility Integrating GeneHancer (GRAIGH), a novel approach to interpreting genome accessibility by integrating information from the GeneHancer database, detailing genome-wide enhancer-to-gene associations. Initially, we outline the methods for integrating GeneHancer with scATAC-seq data. This involves creating a new matrix where GeneHancer element IDs replace traditional accessibility peaks as features. Subsequently, the paper assesses the method’s ability to analyze data and detect cellular heterogeneity. Notably, our findings demonstrate the selective accessibility of GeneHancer elements for distinct cell types, with connected genes serving as precise marker genes. Furthermore, we explore the specificity of GeneHancer element accessibility, highlighting their high selectivity against gene activity. This investigation underscores the potential of Gene Regulation Accessibility Integrating GeneHancer in unraveling the complexities of chromatin accessibility, offering insights into the nuanced relationship between accessibility and cellular heterogeneity

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