ArticlePloS one2009
Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of dispensable essential genes and their interactions with bypass suppressors.Life science alliance · 2024Pooled it
- RebL1 is required for macronuclear structure stability and gametogenesis inMarine life science & technology · 2024Article
- Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.Nature communications · 2023Article
- Opposing Roles of FACT for Euchromatin and Heterochromatin in Yeast.Biomolecules · 2023Review
- The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast.International journal of molecular sciences · 2021Article
- Generating topological protein interaction scores and data visualization with TopS.Methods (San Diego, Calif.) · 2020Article
- Rpd3L HDAC links H3K4me3 to transcriptional repression memory.Nucleic acids research · 2018Article
- Identification of Topological Network Modules in Perturbed Protein Interaction Networks.Scientific reports · 2017Article
- Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex.The Journal of biological chemistry · 2016Article
- Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components.Molecular & cellular proteomics : MCP · 2016Article
- Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network.Molecular & cellular proteomics : MCP · 2014Article
- Article
- Quantitative proteomics demonstrates that the RNA polymerase II subunits Rpb4 and Rpb7 dissociate during transcriptional elongation.Molecular & cellular proteomics : MCP · 2013Article
- Review
- Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions.FEBS letters · 2012Review
- Article
- Review
- Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy.Molecular & cellular proteomics : MCP · 2012Article
- Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.Molecular & cellular proteomics : MCP · 2012Article
- Building protein-protein interaction networks with proteomics and informatics tools.The Journal of biological chemistry · 2011Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Protein complexes are key molecular machines executing a variety of essential cellular processes. Despite the availability of genome-wide protein-protein interaction studies, determining the connectivity between proteins within a complex remains a major challenge. Here we demonstrate a method that is able to predict the relationship of proteins within a stable protein complex. We employed a combination of computational approaches and a systematic collection of quantitative proteomics data from wild-type and deletion strain purifications to build a quantitative deletion-interaction network map and subsequently convert the resulting data into an interdependency-interaction model of a complex. We applied this approach to a data set generated from components of the Saccharomyces cerevisiae Rpd3 histone deacetylase complexes, which consists of two distinct small and large complexes that are held together by a module consisting of Rpd3, Sin3 and Ume1. The resulting representation reveals new protein-protein interactions and new submodule relationships, providing novel information for mapping the functional organization of a complex.
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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.