Thinking BIG rheumatology: how to make functional genomics data work for you

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

ISSN: 1478-6362