Affiliations: Department of Life Science, National Central
University, Taiwan | Department of Computer Science and Information
Engineering, National Central University, Taiwan | Institute of Biochemistry, National Yang-Ming
University, Taiwan | Bioinformatics Center, National Yang-Ming University,
Taiwan E-mail: [email protected]
Abstract: The availability of genome-wide gene expression data provides a
unique set of genes from which we can decipher the mechanisms underlying the
common transcriptional response. Transcription factors, which can bind to
specific DNA sites, cooperatively regulate the transcription of genes. This
study attempts to mine putative binding sites to investigate how combinations
of the sites predicted from known sites and over-represented repetitive
elements are distributed in the promoter regions of groups of functionally
related genes. The over-represented repetitive elements appearing in the
associations are possible transcription factor binding sites. The deduced
association rules would facilitate to predict putative regulatory elements and
to identify genes which are potentially co-regulated by the putative regulatory
elements. Our proposed approach is applied to Saccharomyces cerevisiae and the
promoter regions of yeast ORFs.
Keywords: regulatory elements, repetitive oligonucleotide, data mining, promoter
