Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
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DOI：
10.1186/1752-0509-4-68
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发表时间：
2010-05-25
影响因子：
--
通讯作者：
Nielsen J
中科院分区：
文献类型：
--
作者：
Nandy SK;Jouhten P;Nielsen J
已经使用不同的高通量实验技术对酿酒酵母进行了几项蛋白质-蛋白质相互作用的研究。所有这些结果都收集在BioGRID数据库中，SGD数据库提供了不同蛋白质的详细注释。尽管BioGRID对于研究蛋白质-蛋白质相互作用具有价值，但仍需要手动管理这些相互作用以消除假阳性。在这里，我们描述了一个注释重建的蛋白质-蛋白质相互作用周围的四个关键的营养传感和代谢调节信号转导途径（STP）在酿酒酵母。重建的STP网络包括一个完整的蛋白质-蛋白质相互作用网络，包括关键节点Snf 1，Tor 1，Hog 1和Pka 1。该网络包括总共623个结构开放阅读框架（ORF）和779个蛋白质-蛋白质相互作用。许多蛋白质被鉴定为与一种以上的蛋白激酶具有相互作用。完全重建的相互作用网络包括在单独的数据库中可用于网络中所包括的所有蛋白质（节点）以及它们之间的所有相互作用（边）的所有信息。注释的信息是很容易利用网络建模工具，如Cytoscape和CellDesigner的功能。已报道的完全注释的相互作用模型可作为一个平台，为综合系统生物学研究的营养传感和调控在S。啤酒。此外，我们提出了这个注释的重建作为第一步，在这个酵母中产生一个广泛的注释蛋白质-蛋白质相互作用网络的信号转导和代谢调控。
Several 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. Here 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. The 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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影响因子：
5.3
作者：
Ciesla, Malgorzata;Towpik, Joanna;Boguta, Magdalena
通讯作者：
Boguta, Magdalena
影响因子：
3
作者：
Lin N;Wu B;Jansen R;Gerstein M;Zhao H
通讯作者：
Zhao H
影响因子：
7
作者：
Collins, Sean R.;Kemmeren, Patrick;Krogan, Nevan J.
通讯作者：
Krogan, Nevan J.
影响因子：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP
影响因子：
--
作者：
Castrillo, Juan I;Zeef, Leo A;Hoyle, David C;Zhang, Nianshu;Hayes, Andrew;Gardner, David Cj;Cornell, Michael J;Petty, June;Hakes, Luke;Wardleworth, Leanne;Rash, Bharat;Brown, Marie;Dunn, Warwick B;Broadhurst, David;O'Donoghue, Kerry;Hester, Svenja S;Dunkley, Tom Pj;Hart, Sarah R;Swainston, Neil;Li, Peter;Gaskell, Simon J;Paton, Norman W;Lilley, Kathryn S;Kell, Douglas B;Oliver, Stephen G
通讯作者：
Oliver, Stephen G