Comparative Analysis of Multiple Genome-Scale Data Sets

  1. Margaret Werner-Washburne1,3,
  2. Brian Wylie2,
  3. Kevin Boyack2,
  4. Edwina Fuge1,
  5. Judith Galbraith1,
  6. Jose Weber1, and
  7. George Davidson2
  1. 1Biology Department, University of New Mexico, Albuquerque, New Mexico 87131, USA; 2Sandia National Laboratories, Albuquerque, New Mexico 87185, USA

Abstract

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 G0exit 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 athttp://www.genome.org and athttp://biology.unm.edu/biology/maggieww/Public_Html/Visualcomparison.htm, including data sets and download information for VxInsight.]

Footnotes

  • 3 Corresponding author.

  • E-MAIL maggieww{at}unm.edu; FAX (505) 277-0304.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.225402.

    • Received November 26, 2001.
    • Accepted July 31, 2002.
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