ArticlePLoS computational biology2011
Measuring the evolutionary rewiring of biological networks.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma.PloS one · 2015Pooled it
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- Wiring Between Close Nodes in Molecular Networks Evolves More Quickly Than Between Distant Nodes.Molecular biology and evolution · 2024Article
- Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes.Nucleic acids research · 2022Article
- Using Synthetic Genetic Interactions in Candida glabrata as a Novel Method to Detect Genes with Roles in Antifungal Drug Resistance.Methods in molecular biology (Clifton, N.J.) · 2022Article
- JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics.Journal of visualized experiments : JoVE · 2021Article
- TopicNet: a framework for measuring transcriptional regulatory network change.Bioinformatics (Oxford, England) · 2020Article
- Robustness to extinction and plasticity derived from mutualistic bipartite ecological networks.Scientific reports · 2020Article
- Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.Nucleic acids research · 2020Article
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- Attenuating the emergence of anti-fungal drug resistance by harnessing synthetic lethal interactions in a model organism.PLoS genetics · 2019Article
- Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes.Nucleic acids research · 2019Article
- Network Modeling Unravels Mechanisms of Crosstalk between Ethylene and Salicylate Signaling in Potato.Plant physiology · 2018Article
- The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism.G3 (Bethesda, Md.) · 2017Article
- Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes.PloS one · 2017Article
- SalmoNet, an integrated network of tenNPJ systems biology and applications · 2017Article
- Exploring the interactions of the RAS family in the human protein network and their potential implications in RAS-directed therapies.Oncotarget · 2016Article
- Network biology concepts in complex disease comorbidities.Nature reviews. Genetics · 2016Review
- Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.Biology · 2016Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have accumulated a large amount of biological network data and expect even more to come. Soon, we anticipate being able to compare many different biological networks as we commonly do for molecular sequences. It has long been believed that many of these networks change, or "rewire", at different rates. It is therefore important to develop a framework to quantify the differences between networks in a unified fashion. We developed such a formalism based on analogy to simple models of sequence evolution, and used it to conduct a systematic study of network rewiring on all the currently available biological networks. We found that, similar to sequences, biological networks show a decreased rate of change at large time divergences, because of saturation in potential substitutions. However, different types of biological networks consistently rewire at different rates. Using comparative genomics and proteomics data, we found a consistent ordering of the rewiring rates: transcription regulatory, phosphorylation regulatory, genetic interaction, miRNA regulatory, protein interaction, and metabolic pathway network, from fast to slow. This ordering was found in all comparisons we did of matched networks between organisms. To gain further intuition on network rewiring, we compared our observed rewirings with those obtained from simulation. We also investigated how readily our formalism could be mapped to other network contexts; in particular, we showed how it could be applied to analyze changes in a range of "commonplace" networks such as family trees, co-authorships and linux-kernel function dependencies.
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