Time course regulatory analysis based on paired expression and chromatin accessibility data.

ABSTRACT: A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility data from a time course. TimeReg can be used to prioritize regulatory elements, to extract core regulatory modules at each time point, to identify key regulators driving changes of the cellular state, and to causally connect the modules across different time points. We applied the method to analyze paired chromatin accessibility and gene expression data from a retinoic acid (RA)-induced mouse embryonic stem cells (mESCs) differentiation experiment. The analysis ide

SUBMITTER: Duren Z 

PROVIDER: S-EPMC7197475 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature