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

Schematic overview of Time Course Regulatory Analysis (TimeReg) based on paired gene expression and chromatin accessibility data. (A) TimeReg proposes a three-step framework to infer a high-quality gene regulatory network. Step 1: PECA2 infers context-specific GRN from matched ATAC-seq and RNA-seq data at a single time point to output TF-TG and RE-TG regulatory matrix. Step 2: NMF decomposes the regulatory matrix and extracts the core regulatory modules at each time point. Step 3: Driver regulators are identified (Methods). (B) Overview of PECA2 method. (C) Schematic overview of the major results on two data sets.