Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.
comparative transcriptomics
evolution
gene co-expression networks
gene expression
network alignment
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2021
2021
Historique:
received:
14
04
2021
accepted:
19
07
2021
entrez:
6
9
2021
pubmed:
7
9
2021
medline:
7
9
2021
Statut:
epublish
Résumé
Similarities and differences in the associations of biological entities among species can provide us with a better understanding of evolutionary relationships. Often the evolution of new phenotypes results from changes to interactions in pre-existing biological networks and comparing networks across species can identify evidence of conservation or adaptation. Gene co-expression networks (GCNs), constructed from high-throughput gene expression data, can be used to understand evolution and the rise of new phenotypes. The increasing abundance of gene expression data makes GCNs a valuable tool for the study of evolution in non-model organisms. In this paper, we cover motivations for why comparing these networks across species can be valuable for the study of evolution. We also review techniques for comparing GCNs in the context of evolution, including local and global methods of graph alignment. While some protein-protein interaction (PPI) bioinformatic methods can be used to compare co-expression networks, they often disregard highly relevant properties, including the existence of continuous and negative values for edge weights. Also, the lack of comparative datasets in non-model organisms has hindered the study of evolution using PPI networks. We also discuss limitations and challenges associated with cross-species comparison using GCNs, and provide suggestions for utilizing co-expression network alignments as an indispensable tool for evolutionary studies going forward.
Identifiants
pubmed: 34484293
doi: 10.3389/fgene.2021.695399
pmc: PMC8414652
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
695399Informations de copyright
Copyright © 2021 Ovens, Eames and McQuillan.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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