- Article -
| In Silico Biology 2, 0025 (2002); ©2002, Bioinformation Systems e.V. |
Mining putative regulatory elements in promoter regions of Saccharomyces cerevisiae
Jorng-Tzong Horng1,2, Hsien-Da Huang2, Shir-Ly Huang1,
Ueng-Cheng Yang3,4 and Yu-Chang Chang3
1Department of Life Science, 2Department of Computer Science and Information Engineering, National Central University, Taiwan
3Institute of Biochemistry, 4Bioinformatics Center, National Yang-Ming University, Taiwan
E-mail: horng@db.csie.ncu.edu.tw
Edited by E. Wingender; received November 30, 2001; revised and accepted April 04, 2002; published May 26, 2002
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.
Key words: regulatory elements, data mining, promoter, repetitive oligonucleotide