ArticleProceedings of the National Academy of Sciences of the United States of America2008
The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Evolutionary causes and consequences of gene duplication.Nature reviews. Genetics · 2026Review
- Retention of duplicated genes in evolution.Trends in genetics : TIG · 2022Review
- The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs.eLife · 2019Article
- Build to understand: synthetic approaches to biology.Integrative biology : quantitative biosciences from nano to macro · 2016Review
- Article
- Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts.Scientific reports · 2015Article
- Two Cdc2 Kinase Genes with Distinct Functions in Vegetative and Infectious Hyphae in Fusarium graminearum.PLoS pathogens · 2015Article
- Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts.BMC evolutionary biology · 2015Article
- Article
- Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2014Review
- The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks.PloS one · 2013Article
- Expression of heat shock protein (Hsp90) paralogues is regulated by amino acids in skeletal muscle of Atlantic salmon.PloS one · 2013Article
- Positionally biased gene loss after whole genome duplication: evidence from human, yeast, and plant.Genome research · 2012Article
- Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods.Protein science : a publication of the Protein Society · 2012Review
- Measuring the evolutionary rewiring of biological networks.PLoS computational biology · 2011Article
- Article
- Genetic interactions reveal the evolutionary trajectories of duplicate genes.Molecular systems biology · 2010Article
- Yeast evolutionary genomics.Nature reviews. Genetics · 2010Review
- Distinct phosphatase requirements and GATA factor responses to nitrogen catabolite repression and rapamycin treatment in Saccharomyces cerevisiae.The Journal of biological chemistry · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Gene duplication is an important mechanism in the evolution of protein interaction networks. Duplications are followed by the gain and loss of interactions, rewiring the network at some unknown rate. Because rewiring is likely to change the distribution of network motifs within the duplicated interaction set, it should be possible to study network rewiring by tracking the evolution of these motifs. We have developed a mathematical framework that, together with duplication data from comparative genomic and proteomic studies, allows us to infer the connectivity of the preduplication network and the changes in connectivity over time. We focused on the whole-genome duplication (WGD) event in Saccharomyces cerevisiae. The model allowed us to predict the frequency of intergene interaction before WGD and the post duplication probabilities of interaction gain and loss. We find that the predicted frequency of self-interactions in the preduplication network is significantly higher than that observed in today's network. This could suggest a structural difference between the modern and ancestral networks, preferential addition or retention of interactions between ohnologs, or selective pressure to preserve duplicates of self-interacting proteins.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.