Strategies and tools for upgrading the information content of regulated gene lists from microarray experiments

The transcriptional profiling of whole genomes using cDNA or oligonucleotide high-density arrays is becoming increasingly popular among the biomedical research community. Although advances in technology and the rapid rise in microarray data availability are leading to new insight into fundamental biological problems, investigators are still confronted with the major problem of upgrading the information content of regulated gene lists obtained from microarray experiments. indeed, the efficient exploitation of gene expression databases requires not only computational tools for management and analysis of primary data, but also integrating lists of modulated genes with of other sources of biological information, such as biochemical pathways and biomedical literature. However, such integration, essential to functionally interpret derived gene lists and to relate expression profiles to molecular physiology, often results in an explosion of the information content instead of knowledge growth. This article reviews several public resources for visualization, annotation, and functional interpretation of gene expression datasets. The focus is on tools that integrate functional genomic information, biochemical pathways, and bibliographic records with intuitive graphical summaries.