title: Co-expression networks: graph properties and topological comparisons.
abstract: BACKGROUND
  Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are 'functionally' related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known biological networks. In this article, we aim at investigating the structural properties of co-expression networks inferred for the species Saccharomyces Cerevisiae and comparing them with the topological properties of the known, well-established transcriptional network, MIPS physical network and protein-protein interaction (PPI) network of yeast.
  
  
  RESULTS
  These topological comparisons indicate that co-expression networks are not distinctly related with either the PPI or the MIPS physical interaction networks, showing important structural differences between them. When focusing on a more literal comparison, vertex by vertex and edge by edge, the conclusion is the same: the fact that two genes exhibit a high gene expression correlation degree does not seem to obviously correlate with the existence of a physical binding between the proteins produced by these genes or the existence of a MIPS physical interaction between the genes. The comparison of the yeast regulatory network with inferred yeast co-expression networks would suggest, however, that they could somehow be related.
  
  
  CONCLUSIONS
  We conclude that the gene expression-based co-expression networks reflect more on the gene regulatory networks but less on the PPI or MIPS physical interaction networks.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
authors.forename: Ramon
authors.initials: R
authors.lastname: Xulvi-Brunet
authors.forename: Hongzhe
authors.initials: H
authors.lastname: Li
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000378:metabolism