Sc-compReg Enables the Comparison of Gene Regulatory Networks Between Conditions Using Single-cell Data

Overview

Journal Nat Commun

Specialty Biology

Date 2021 Aug 7

PMID 34362918

Citations 16

Authors

Zhana Duren

Wenhui Sophia Lu

Joseph G Arthur

Preyas Shah

Jingxue Xin

Francesca Meschi

Miranda Lin Li

Corey M Nemec

Yifeng Yin

Wing Hung Wong

Affiliations

Soon will be listed here.

Abstract

The comparison of gene regulatory networks between diseased versus healthy individuals or between two different treatments is an important scientific problem. Here, we propose sc-compReg as a method for the comparative analysis of gene expression regulatory networks between two conditions using single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq). Our software, sc-compReg, can be used as a stand-alone package that provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and the construction of differential regulatory networks across two conditions. We apply the method to compare the gene regulatory networks of an individual with chronic lymphocytic leukemia (CLL) versus a healthy control. The analysis reveals a tumor-specific B cell subpopulation in the CLL patient and identifies TOX2 as a potential regulator of this subpopulation.

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