Title: Identification of temporal network changes in short-course gene expression from C. elegans reveals structural volatility
Authors: Kathryn Cooper; Wail Hassan; Hesham Ali
Addresses: College of Information Science and Technology, University of Nebraska at Omaha, 1110 S. 67th St., Omaha, NE 68182, USA ' Department of Biomedical Sciences, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street M3-417 Kansas City, MO 64108, USA ' College of Information Science and Technology, University of Nebraska at Omaha, 1110 S. 67th St., Omaha, NE 68182, USA
Abstract: Many bioinformatics algorithms attempt to extract relevant biological information from datasets obtained at specific data points. However, it is critical to identify changing genes in temporal data so that studies can focus on the dynamics of gene expression. While networks continue to play a significant role in characterising biological relationships, most biomedical network modelling studies focus on 'static' network-based analysis. In this study, we use a temporal, network-based approach to identify and rank genes that exhibit variation in short-course gene expression. We use a Caenorhabditis elegans (C. elegans) gene correlation network obtained from mRNA expression to illustrate the value of the proposed approach, and compare the results of this method to results obtained from traditional differential gene expression analysis. We show that temporal network analysis identifies genes that are inherently different from differentially expressed genes, raising new questions about structural meaning in expression networks and how changes in expression are observed.
Keywords: temporal network analysis; gene expression; correlation networks; reliability; node ranking.
International Journal of Computational Biology and Drug Design, 2019 Vol.12 No.2, pp.171 - 188
Received: 28 Feb 2018
Accepted: 27 Jun 2018
Published online: 11 May 2019 *