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Vol. 12, Issue 10, 1564-1573, October 2002

METHODS
Comparative Analysis of Multiple Genome-Scale Data Sets

Margaret Werner-Washburne,1,3 Brian Wylie,2 Kevin Boyack,2 Edwina Fuge,1 Judith Galbraith,1 Jose Weber,1 and George Davidson2

1 Biology Department, University of New Mexico, Albuquerque, New Mexico 87131, USA; 2 Sandia National Laboratories, Albuquerque, New Mexico 87185, USA

The ongoing analyses of published genome-scale data sets is evidence that different approaches are required to completely mine this data. We report the use of novel tools for both visualization and data set comparison to analyze yeast gene-expression (cell cycle and exit from stationary phase/G0) and protein-interaction studies. This analysis led to new insights about each data set. For example, G1-regulated genes are not co-regulated during exit from stationary phase, indicating that the cells are not synchronized. The tight clustering of other genes during exit from stationary-phase data set further indicates the physiological responses during G0 exit are separable from cell-cycle events. Comparison of the two data sets showed that ribosomal-protein genes cluster tightly during exit from stationary phase, but are found in three significantly different clusters in the cell-cycle data set. Two protein-interaction data sets were also compared with the gene-expression data. Visual analysis of the complete data sets showed no clear correlation between co-expression of genes and protein interactions, in contrast to published reports examining subsets of the protein-interaction data. Neither two-hybrid study identified a large number of interactions between ribosomal proteins, consistent with recent structural data, indicating that for both data sets, the identification of false-positive interactions may be lower than previously thought.

[Supplemental material is available online at http://www.genome.org and at http://biology.unm.edu/biology/maggieww/Public_Html/Visualcomparison.htm, including data sets and download information for VxInsight.]

3 Corresponding author.

12:1564-1573 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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