title: Complementary techniques of clustering and composite pattern analysis to Saccharomyces cerevisiae gene expression.
abstract: We present the combined application of clustering and composite pattern analysis to Saccharomyces cerevisiae gene expression and sequence data. The aim is to devise a system for the efficient investigation of the upstream regions associated with regulating the coordinated transcriptional response of genes via the location of cis-acting elements. The clustering algorithm presented allows clusters to overlap in light of the fact that many genes are regulated by multiple factors and/or are associated with multiple functions in the organism. The sequence clusters are analysed for shared monad and dyad patterns. These motifs are commonly regarded as putative cis-acting regulatory elements. Computationally, dyad patterns may be difficult and expensive to discover and verify if the sequences are very large. This has highlighted the need to obtain maximally--with regards to the pattern in question--'enriched' sets of sequences to uncover these motifs. We present overlapping clusters as an ideal basis for the discovery of conserved motifs.
authors.affiliation: Genesis Research and Development Corporation Limited, and Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland, New Zealand. magusin@xtra.co.nz
authors.forename: Andreas
authors.initials: A
authors.lastname: Magusin
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence / Q000235:genetics; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D005809:Genes, Regulator / Q000235:genetics; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D029701:Saccharomyces cerevisiae Proteins