Using OmicsNet for Network Integration and 3D Visualization

Guangyan Zhou; Jianguo Xia

doi:10.1002/cpbi.69

Using OmicsNet for Network Integration and 3D Visualization

Curr Protoc Bioinformatics. 2019 Mar;65(1):e69. doi: 10.1002/cpbi.69. Epub 2018 Dec 17.

Authors

Guangyan Zhou¹, Jianguo Xia^{1

2

3}

Affiliations

¹ Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Quebec, Canada.
² Department of Animal Sciences, McGill University, Sainte Anne de Bellevue, Quebec, Canada.
³ Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada.

PMID: 30556956
DOI: 10.1002/cpbi.69

Abstract

OmicsNet is a novel web-based tool for creating and visualizing complex biological networks in 3D space. By coupling a comprehensive knowledgebase with the powerful WebGL technology, OmicsNet allows researchers to intuitively explore molecular interactions and regulatory relationships among genes, transcription factors, microRNAs, and metabolites. OmicsNet fills an important gap by facilitating multi-omics integration and systems biology. This article contains three basic protocols covering the key features of OmicsNet, including how to create biological networks from a single or multiple list(s) of molecules, how to integrate or enrich different types of networks, and how to navigate the 3D visualization system to obtain biological insights. The OmicsNet web server is freely available at https://www.omicsnet.ca. © 2018 by John Wiley & Sons, Inc.

Keywords: 3D network visualization; PPI; TF-gene interactions; metabolic network; miRNA-gene interactions; multi-omics integration; network analysis; web application.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Regulatory Networks*
Imaging, Three-Dimensional*
Protein Interaction Maps
Software*