Nucleic Acids Research Advance Access originally published online on December 4, 2008
Nucleic Acids Research 2009 37(2):526-532; doi:10.1093/nar/gkn972
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Nucleic Acids Research, 2009, Vol. 37, No. 2 526-532
© 2008 The Author(s)
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.
Computational Biology |
Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae
1Biostatistics Department, School of Public Health, Boston University, MA 02118, USA, 2Institute of Statistical Science, Academia Sinica, Taiwan and 3Statistics Department, University of California, Los Angeles, CA 90095, USA
*To whom correspondence should be addressed. Tel: +1 310 825 4897; Fax: +1 310 206 5658; Email: kcli{at}stat.ucla.edu
Received August 5, 2008. Revised October 30, 2008. Accepted November 18, 2008.
Many successful functional studies by gene expression profiling in the literature have led to the perception that profile similarity is likely to imply functional association. But how true is the converse of the above statement? Do functionally associated genes tend to be co-regulated at the transcription level? In this paper, we focus on a set of well-validated yeast protein complexes provided by Munich Information Center for Protein Sequences (MIPS). Using four well-known large-scale microarray expression data sets, we computed the correlations between genes from the same complex. We then analyzed the relationship between the distribution of correlations and the complex size (the number of genes in a protein complex). We found that except for a few large protein complexes, such as mitochondrial ribosomal and cytoplasmic ribosomal proteins, the correlations are on the average not much higher than that from a pair of randomly selected genes. The global impact of large complexes on the expression of other genes in the genome is also studied. Our result also showed that the expression of over 85% of the genes are affected by six large complexes: the cytoplasmic ribosomal complex, mitochondrial ribosomal complex, proteasome complex, F0/F1 ATP synthase (complex V) (size 18), rRNA splicing (size 24) and H+- transporting ATPase, vacular (size 15).
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