Elisabetta Manduchi, Ph.D.
Research Project Manager
Computational Biology and Informatics Laboratory
Center for Bioinformatics
Challenges in the analysis of microarray data and an approach to collection, organization, and exchange of all relevant information
In the past few years gene expression microarray technology has become more widespread and many laboratories are now conducting studies using gene expression arrays of various kinds, recognizing the promise of this technology. The first published works utilizing gene expression arrays applied them right away to tackle specific biological questions (e.g. discovery of co-regulated genes), therefore their computational focus was mostly on down-stream analyses (e.g. clustering). But the challenges posed by this kind of experiment, from the perspectives of bench work and computational analysis, are many. In particular, as the technology has become more widely used and more studies have been carried out, investigators have become increasingly aware of the need to devote more efforts to bench protocol optimization and to low-level analyses (e.g. image quantification, quality control and normalization), in order to minimize up-stream problems which could have cascading effects that would hamper the biological conclusions that are made. Moreover, both bench biologists and bioinformaticians have come to increasingly appreciate the importance of collaborating closely, starting from the onset of a study, including array and experimental design. Several groups have therefore begun focusing part of their work on development of suitable infrastructures to facilitate intelligent management and exchange of all the crucial information related to microarray studies, in order to enable adequate analyses and to exploit this technology to its fullest. In this talk I will illustrate some of the tools and protocols that we have developed to this end; also demonstrating them through some case-specific studies.