AUTHOR=Ramos Pablo Ivan Pereira , Arge Luis Willian Pacheco , Lima Nicholas Costa Barroso , Fukutani Kiyoshi F. , de Queiroz Artur Trancoso L. 

TITLE=Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01120

DOI=10.3389/fgene.2019.01120

ISSN=1664-8021

ABSTRACT=<p>Recent technological advances for the acquisition of multi-<italic>omics</italic> data have allowed an unprecedented understanding of the complex intricacies of biological systems. In parallel, a myriad of computational analysis techniques and bioinformatics tools have been developed, with many efforts directed towards the creation and interpretation of networks from this data. In this review, we begin by examining key network concepts and terminology. Then, computational tools that allow for their construction and analysis from high-throughput <italic>omics</italic> datasets are presented. We focus on the study of functional relationships such as co-expression, protein–protein interactions, and regulatory interactions that are particularly amenable to modeling using the framework of networks. We envisage that many potential users of these analytical strategies may not be completely literate in programming languages and code adaptation, and for this reason, emphasis is given to tools’ user-friendliness, including plugins for the widely adopted Cytoscape software, an open-source, cross-platform tool for network analysis, visualization, and data integration.</p>