Abstract
BACKGROUND: Gene set analysis is considered to be a way of improving our biological interpretation of the observed expression patterns. This paper describes different methods applied to analyse expression data from a chicken DNA microarray dataset. RESULTS: Applying different gene set analyses to the chicken expression data led to different ranking of the Gene Ontology terms tested. A method for prediction of possible annotations was applied. CONCLUSION: Biological interpretation based on gene set analyses dependent on the statistical method used. Methods for predicting the possible annotations for genes with unknown function from the expression data at hand could be useful, but our results indicate that careful validation of the predictions is needed.