BayGO: Bayesian analysis of ontology term enrichment in microarray data

Abstract Background The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. Results BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. Conclusion The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one to measure the statistical association between generic ontology terms and differential expression, instead of working only with the common significance analysis.

We thank Thiago M. Venancio for several suggestions and critical reading of the manuscript. TK is supported by a doctoral fellowship from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP). SLG and CABP are partially supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).

We thank Thiago M. Venancio for several suggestions and critical reading of the manuscript. TK is supported by a doctoral fellowship from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP). SLG and CABP are partially supported by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).