ArticleMolecular systems biology2007
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks.
Article in Molecular systems biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- A novel ILP framework to identify compensatory pathways in genetic interaction networks with GIDEON.Bioinformatics (Oxford, England) · 2026Article
- A Novel ILP Framework to Identify Compensatory Pathways in Genetic Interaction Networks with GIDEON.bioRxiv : the preprint server for biology · 2026Article
- Exploring weighting schemes for the discovery of informative generalized between pathway models to uncover pathways in genetic interaction networks.Scientific reports · 2025Article
- Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs.PLoS computational biology · 2023Article
- Using dual-network-analyser for communities detecting in dual networks.BMC bioinformatics · 2022Article
- Yeast Sphingolipid Phospholipase GeneMolecular and cellular biology · 2020Article
- Identification of prognosis-related genes and construction of multi-regulatory networks in pancreatic cancer microenvironment by bioinformatics analysis.Cancer cell international · 2020Article
- Contributions of Gene Modules Regulated by Essential Noncoding RNA in Colon Adenocarcinoma Progression.BioMed research international · 2020Article
- Predicting synthetic lethal interactions using conserved patterns in protein interaction networks.PLoS computational biology · 2019Article
- Integrated Analysis of Brain Transcriptome Reveals Convergent Molecular Pathways in Autism Spectrum Disorder.Frontiers in psychiatry · 2019Article
- Integrated multifactor analysis explores core dysfunctional modules in autism spectrum disorder.International journal of biological sciences · 2018Article
- A multidimensional integration analysis reveals potential bridging targets in the process of colorectal cancer liver metastasis.PloS one · 2017Article
- Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification.Briefings in bioinformatics · 2016Article
- Revealing potential molecular targets bridging colitis and colorectal cancer based on multidimensional integration strategy.Oncotarget · 2015Article
- A functional module-based exploration between inflammation and cancer in esophagus.Scientific reports · 2015Article
- Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer.Biology direct · 2015Article
- Detection of composite communities in multiplex biological networks.Scientific reports · 2015Article
- A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.Journal of neuroscience research · 2015Article
- ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system.Autophagy · 2015Article
- Single nucleotide variations: biological impact and theoretical interpretation.Protein science : a publication of the Protein Society · 2014Review
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The biological interpretation of genetic interactions is a major challenge. Recently, Kelley and Ideker proposed a method to analyze together genetic and physical networks, which explains many of the known genetic interactions as linking different pathways in the physical network. Here, we extend this method and devise novel analytic tools for interpreting genetic interactions in a physical context. Applying these tools on a large-scale Saccharomyces cerevisiae data set, our analysis reveals 140 between-pathway models that explain 3765 genetic interactions, roughly doubling those that were previously explained. Model genes tend to have short mRNA half-lives and many phosphorylation sites, suggesting that their stringent regulation is linked to pathway redundancy. We also identify 'pivot' proteins that have many physical interactions with both pathways in our models, and show that pivots tend to be essential and highly conserved. Our analysis of models and pivots sheds light on the organization of the cellular machinery as well as on the roles of individual proteins.
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