ArticleNucleic acids research2009
Construction and application of a protein and genetic interaction network (yeast interactome).
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression.BMC medical genomics · 2014Article
- Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae.Nucleic acids research · 2013Article
- Article
- Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.Molecular & cellular proteomics : MCP · 2012Article
- Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae.Mitochondrion · 2009Article
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Authors and funding
3 authors.
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Abstract
Cytoscape is a bioinformatic data analysis and visualization platform that is well-suited to the analysis of gene expression data. To facilitate the analysis of yeast microarray data using Cytoscape, we constructed an interaction network (interactome) using the curated interaction data available from the Saccharomyces Genome Database (www.yeastgenome.org) and the database of yeast transcription factors at YEASTRACT (www.yeastract.com). These data were formatted and imported into Cytoscape using semi-automated methods, including Linux-based scripts, that simplified the process while minimizing the introduction of processing errors. The methods described for the construction of this yeast interactome are generally applicable to the construction of any interactome. Using Cytoscape, we illustrate the use of this interactome through the analysis of expression data from a recent yeast diauxic shift experiment. We also report and briefly describe the complex associations among transcription factors that result in the regulation of thousands of genes through coordinated changes in expression of dozens of transcription factors. These cells are thus able to sensitively regulate cellular metabolism in response to changes in genetic or environmental conditions through relatively small changes in the expression of large numbers of genes, affecting the entire yeast metabolome.
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Registered trials
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