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Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.

ABSTRACT: Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.

SUBMITTER: Duren Z

PROVIDER: S-EPMC9109353 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.

Duren Zhana Z Chang Fengge F Naqing Fnu F Xin Jingxue J Liu Qiao Q Wong Wing Hung WH

Genome biology 20220516 1

Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pear ...[more]

PMID: 35578363

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Author Correction: Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG.

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