Integrative approaches to reconstruct regulatory networks from multi-omics data: A review of state-of-the-art methods

Abstract

Data generation using high throughput technologies has led to the accumulation of diverse types of molecular data. These data have different types (discrete, real, string, etc.) and occur in various formats and sizes. Datasets including gene expression, miRNA expression, protein-DNA binding data (ChIP-Seq/ChIP-ChIP), mutation data (copy number variation, single nucleotide polymorphisms), annotations, interactions, and association data are some of the commonly used biological datasets to study various cellular mechanisms of living organisms. Each of them provides a unique, complementary and partly independent view of the genome and hence embed essential information about the regulatory mechanisms of genes and their products. Therefore, integrating these data and inferring regulatory interactions from them offer a system level of biological insight in predicting gene functions and their phenotypic outcomes. To study genome functionality through regulatory networks, different methods have been proposed for collective mining of information from an integrated dataset. We survey here integration methods that reconstruct regulatory networks using state-of-the-art techniques to handle multi-omics (i.e., genomic, transcriptomic, proteomic) and other biological datasets.

Keywords: Data integration; Gene expression; Network inference; Regulatory networks; Transcription factor.