Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis-driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Because focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the Gene Ontology Consortium nomenclature. We used this tool to compare several arrays focused on apoptosis, oncogenes, and tumor suppressors. We considered arrays from BD Biosciences Clontech, PerkinElmer, Sigma-Genosys, and SuperArray. We showed that among the oncogene arrays, the PerkinElmer MICROMAX oncogene microarray has a better representation of oncogenesis, protein phosphorylation, and negative control of cell proliferation. The comparison of the apoptosis arrays showed that most apoptosis-related biological processes are equally well represented on the arrays considered. However, functional categories such as immune response, cell-cell signaling, cell-surface receptor linked signal transduction, and interleukins are better represented on the Sigma-Genoys Panorama human apoptosis array. At the same time, processes such as cell cycle control, oncogenesis, and negative control of cell proliferation are better represented on the BD Biosciences Clontech Atlas Select human apoptosis array.