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

Autor: Zhana Duren, Fengge Chang, Fnu Naqing, Jingxue Xin, Qiao Liu, Wing Hung Wong
Jazyk: angličtina
Rok vydání: 2022
Předmět:
Zdroj: Genome Biology, Vol 23, Iss 1, Pp 1-19 (2022)
Druh dokumentu: article
ISSN: 1474-760X
DOI: 10.1186/s13059-022-02682-2
Popis: 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.
Databáze: Directory of Open Access Journals
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