Knowledge Discovery for Gene Regulatory Regions Analysis

This paper presents implementation of Data Mining and Knowledge Discovery techniques for analysis of gene regulatory regions. The method is designed to search for regularities in tables of context features of DNA sequences involved in regulation of transcription. The goal is to discover regularities that relate nucleotide sequences to the functional classes of these sequences. The search patterns for regularities are constructed in the first-order logic augmented by probabilistic estimates. A software system "Gene Discovery" has been developed to implement the method. This system accepts molecular-genetical data retrieved from a database by using SQL queries. Nucleotide sequences of promoters of several functional systems were extracted from the TRRD database and analysed. The data include nucleotide sequences of erythroid-specific gene promoters, endocrine system gene promoters, promoter regions of the genes controlling cell cycle, promoter of genes regulating lipid metabolism, and muscle-specific gene promoters. Several regularities that relate the nucleotide sequences in the regulatory DNA with each functional class have been found. A was developed Discovered Using discovered regularities a a recognition procedure was devised.