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BACKGROUND: Gene set analysis is a commonly used method for analysing microarray data by considering groups of functionally related genes instead of individual genes. Here we present the use of two gene set analysis approaches: Globaltest and GOEAST.Globaltest is a method for testing whether sets of genes are significantly associated with a variable of interest. GOEAST is a freely accessible web-based tool to test GO term enrichment within given gene sets. The two approaches were applied in the analysis of gene lists obtained from three different contrasts in a microarray experiment conducted to study the host reactions in broilers following Eimeria infection. RESULTS: The Globaltest identified significantly associated gene sets in one of the three contrasts made in the microarray experiment whereas the functional analysis of the differentially expressed genes using GOEAST revealed enriched GO terms in all three contrasts. CONCLUSION: Globaltest and GOEAST gave different results, probably due to the different algorithms and the different criteria used for evaluating the significance of GO terms.
Hulsegge et al. (Thu,) studied this question.