ArticleGenome research2011
Putting genetic interactions in context through a global modular decomposition.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 75 citations in OpenAlex.
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- Multiple Forms of Multifunctional Proteins in Health and Disease.Frontiers in cell and developmental biology · 2020Review
- Discovering genetic interactions bridging pathways in genome-wide association studies.Nature communications · 2019Article
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- Reusable building blocks in biological systems.Journal of the Royal Society, Interface · 2018Article
- Integrating genetic and protein-protein interaction networks maps a functional wiring diagram of a cell.Current opinion in microbiology · 2018Review
- The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion.The Journal of cell biology · 2018Article
- Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions.Scientific reports · 2018Article
- Systematic analysis of complex genetic interactions.Science (New York, N.Y.) · 2018Article
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- Pathway-based discovery of genetic interactions in breast cancer.PLoS genetics · 2017Article
- Genetic interactions and functional analyses of the fission yeast gsk3 and amk2 single and double mutants defective in TORC1-dependent processes.Scientific reports · 2017Article
- A global genetic interaction network maps a wiring diagram of cellular function.Science (New York, N.Y.) · 2016Article
- Cancer network activity associated with therapeutic response and synergism.Genome medicine · 2016Article
- Similarity analysis between chromosomes of Homo sapiens and monkeys with correlation coefficient, rank correlation coefficient and cosine similarity measures.Genomics data · 2016Article
- Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.Cell systems · 2016Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 3 countries.
Funding
Abstract
Genetic interactions provide a powerful perspective into gene function, but our knowledge of the specific mechanisms that give rise to these interactions is still relatively limited. The availability of a global genetic interaction map in Saccharomyces cerevisiae, covering ∼30% of all possible double mutant combinations, provides an unprecedented opportunity for an unbiased assessment of the native structure within genetic interaction networks and how it relates to gene function and modular organization. Toward this end, we developed a data mining approach to exhaustively discover all block structures within this network, which allowed for its complete modular decomposition. The resulting modular structures revealed the importance of the context of individual genetic interactions in their interpretation and revealed distinct trends among genetic interaction hubs as well as insights into the evolution of duplicate genes. Block membership also revealed a surprising degree of multifunctionality across the yeast genome and enabled a novel association of VIP1 and IPK1 with DNA replication and repair, which is supported by experimental evidence. Our modular decomposition also provided a basis for testing the between-pathway model of negative genetic interactions and within-pathway model of positive genetic interactions. While we find that most modular structures involving negative genetic interactions fit the between-pathway model, we found that current models for positive genetic interactions fail to explain 80% of the modular structures detected. We also find differences between the modular structures of essential and nonessential genes.
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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.