Nucleic Acids Research Advance Access originally published online on March 9, 2009
Nucleic Acids Research 2009 37(7):e54; doi:10.1093/nar/gkp140
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Nucleic Acids Research, 2009, Vol. 37, No. 7 e54
Published by Oxford University Press 2009
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
Construction and application of a protein and genetic interaction network (yeast interactome)
1Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences and 2Life Sciences Division, U.S. Army Research Office, Research Triangle Park, NC 27709, USA
*To whom correspondence should be addressed. Tel: +1 919 541 4792; Fax: +1 919 541 7613; Email: copelan1{at}niehs.nih.gov
Received October 28, 2008. Revised February 18, 2009. Accepted February 19, 2009.
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.