Table 1.

Different assays for functional genomics, common protocols, format of the data after processing, and application to the GRN

Assay	Protocol	Processed data format	Direct application to GRN
Gene expression	RNA-seq, microarray	Table of samples (columns) by genes (rows)	Output
Chromatin state	ChIP-seq, ATAC-seq	List of peaks	Nodes
Chromatin interactions	Hi-C, ChIA-PET, GAM	Matrix of interactions	Edges
DNA methylation	BS-seq	List of methylated sites	Nodes
Single-cell technology	scRNA-seq	Table of cells (columns) by genes (rows)	Discriminate different GRNs

GRN gene regulatory network, RNA-seq RNA-sequencing, ChIP-seq chromatin immunoprecipitation followed by high-throughput sequencing, ATAC-seq Assay for Transposase Accessible Chromatin followed by high-throughput sequencing, Hi-C high-throughput chromosome conformation capture, ChIA-PET Chromatin Interaction Analysis by Paired-End Tag Sequencing, GAM genome architecture mapping, BS-seq bisulfite sequencing, scRNA-seq single-cell RNA-sequencing