title: Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
abstract: BACKGROUND
  The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes into putatively co-regulated groups, as opposed to those that are simply co-expressed. Be cause genes may be co-regulated only across a subset of all observed experimental conditions, biclustering (clustering of genes and conditions) is more appropriate than standard clustering. Co-regulated genes are also often functionally (physically, spatially, genetically, and/or evolutionarily) associated, and such a priori known or pre-computed associations can provide support for appropriately grouping genes. One important association is the presence of one or more common cis-regulatory motifs. In organisms where these motifs are not known, their de novo detection, integrated into the clustering algorithm, can help to guide the process towards more biologically parsimonious solutions.
  
  
  RESULTS
  We have developed an algorithm, cMonkey, that detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs.
  
  
  CONCLUSIONS
  We have applied this procedure to the archaeon Halobacterium NRC-1, as part of our efforts to decipher its regulatory network. In addition, we used cMonkey on public data for three organisms in the other two domains of life: Helicobacter pylori, Saccharomyces cerevisiae, and Escherichia coli. The biclusters detected by cMonkey both recapitulated known biology and enabled novel predictions (some for Halobacterium were subsequently confirmed in the laboratory). For example, it identified the bacteriorhodopsin regulon, assigned additional genes to this regulon with apparently unrelated function, and detected its known promoter motif. We have performed a thorough comparison of cMonkey results against other clustering methods, and find that cMonkey biclusters are more parsimonious with all available evidence for co-regulation.
authors.affiliation: Institute for Systems Biology, 1441 N, 34th St, Seattle, WA 98103-8904, USA. dreiss@systemsbiology.org
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation; D016678:Genome; D023281:Genomics / Q000379:methods*; D006217:Halobacterium / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D013045:Species Specificity