Assessing the Functional Bias of Commercial Microarrays Using the Onto-Compare Database

Abstract

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-Genosys 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.

In Silico Gene Selection Strategy for Custom Microarray Design

“…The use of a less stringent threshold value will increase the number of sequences selected, although confidence in the homology of the resulting sequences would diminish. In order to evaluate the functional pathways and biological processes encompassed by the selected gene set, the corresponding source genes were submitted to Onto-Compare (16). This tool is complementary to the gene selection strategy described here, as the results of such an analysis can reveal underrepresented functional categories.…”

“…If the Xenopus sequence was already contained in the database, only the comment field was updated, indicating the sequence was found on multiple input arrays. The Onto-Compare tool was used to evaluate the functional aspects of the selected gene set (16). …”

“…This permits the design of arrays focused on specific functional pathways or biological processes. A related tool, Onto-Compare, gives investigators the ability to perform a functional analysis of numerous commercial chips as well as user-defined custom arrays (15,16). Such an analysis provides a better understanding of the pathways and processes that can be investigated with a given microarray.…”

Microarray RNA transcriptional profiling: Part II. Analytical considerations and annotation

“…To access the biological significance of microarray data, the OC database was developed [77]. The OC database is implemented in Oracle in which a group of Java programs and Perl routines are used to download, parse and update the database.…”

Genomic Research in Eucalyptus

“…From the resulting label intensity of the spot, it can be determined if the gene in question has been up-or down-regulated, or if its expression has remained the same (Thomas & Klaper, 2004). It must be remembered, however, that this technique is limited to the set of genes being tested and is also influenced by which genes have already been isolated from the transcriptome (Draghici et al, 2003). Gene expression studies in eucalypts are summarised in Table 5.…”