Treffer: TECHNICAL REPORT Exploring the Use of Main Memory Database (MMDB) Technology for the Analysis of Gene Expression Microarray Data Prepared by

The high volume and complexity of microarray data has created both opportunities and challenges for bioinformaticians or computational biologists as the genome-wide analysis of expression data requires advanced database, computational, and statistical approaches. This technical report focuses on the database aspect of microarray informatics research. While relational technology predominates as the platform for current microarray database systems, it has limitations when it comes to large-scale and complex analysis of gene expression data. This type of analysis cannot be handled naturally by relational queries. To augment the relational technology, we describe a lightweight but high-performance approach that allows complex microarray data analysis to be efficiently integrated with a main memory database (MMDB) approach, built upon the aggregated main memory of a cluster of computers. To compare the MMDB approach with the relational approach, we have benchmarked the performance of several test queries. The results suggest that the MMDB approach has the potential to achieve a significant speedup for many analytic retrieval queries. 2 1.