ArticleBMC systems biology2010
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
Article in BMC systems biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- An efficient framework for protein-protein interaction prediction by integrating stacked denoising autoencoders and random ferns.iScience · 2026Article
- Integration of multiple stress signals in plants using synthetic Boolean logic gates.Plant physiology · 2023Article
- From Petri Plates to Petri Nets, a revolution in yeast biology.FEMS yeast research · 2022Article
- A study of the Immune Epitope Database for some fungi species using network topological indices.Molecular diversity · 2017Article
- Experimental and computational analysis of a large protein network that controls fat storage reveals the design principles of a signaling network.PLoS computational biology · 2015Article
- Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae.BMC systems biology · 2014Article
- Metabolic activation of the HOG MAP kinase pathway by Snf1/AMPK regulates lipid signaling at the Golgi.Traffic (Copenhagen, Denmark) · 2012Article
- Systems biology: new institute and applications.The Yale journal of biology and medicine · 2011Article
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3 authors.
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Abstract
backgroundSeveral protein-protein interaction studies have been performed for the yeast Saccharomyces cerevisiae using different high-throughput experimental techniques. All these results are collected in the BioGRID database and the SGD database provide detailed annotation of the different proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives.
resultsHere we describe an annotated reconstruction of the protein-protein interactions around four key nutrient-sensing and metabolic regulatory signal transduction pathways (STP) operating in Saccharomyces cerevisiae. The reconstructed STP network includes a full protein-protein interaction network including the key nodes Snf1, Tor1, Hog1 and Pka1. The network includes a total of 623 structural open reading frames (ORFs) and 779 protein-protein interactions. A number of proteins were identified having interactions with more than one of the protein kinases. The fully reconstructed interaction network includes all the information available in separate databases for all the proteins included in the network (nodes) and for all the interactions between them (edges). The annotated information is readily available utilizing the functionalities of network modelling tools such as Cytoscape and CellDesigner.
conclusionsThe reported fully annotated interaction model serves as a platform for integrated systems biology studies of nutrient sensing and regulation in S. cerevisiae. Furthermore, we propose this annotated reconstruction as a first step towards generation of an extensive annotated protein-protein interaction network of signal transduction and metabolic regulation in this yeast.
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