Inference and Analysis of Gene Regulatory Networks in R

This chapter presents the basic steps that are required to conduct a genome-scale gene regulatory networks (GRN) inference and network-based functional analysis in an R programming environment. The analysis is performed for a large-scale multiple myeloma gene expression data set. It shows the retrieval of gene expression data sets from the NCBI "GeoDB" database, their preprocessing and probe set summarization for gene annotation based on "Entrez" gene identifiers and gene symbols. The first step for the inference of a GRN is the data retrieval and data preprocessing. The chapter uses a publicly available preprocessed multiple myeloma data set available from "GeoDB" with the accession "GSE4581". The chapter gives basic gene expression data processing requirements for the inference and analysis of GRN by the application of the "bc3net" R package. The "bc3net" is a bagging approach of the "c3net" and aggregates an ensemble of "c3net" GRN that are inferred by bootstrapping a gene expression data set.