Complementary techniques of clustering and composite pattern analysis to Saccharomyces cerevisiae gene expression.
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.
Magusin
Andreas
A
Genesis Research and Development Corporation Limited, and Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland, New Zealand. magusin@xtra.co.nz
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*
D029701:Saccharomyces cerevisiae Proteins