Gene set analysis methods applied to chicken microarray expression dataReport as inadecuate

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BMC Proceedings

, 3:S8

First Online: 16 July 2009DOI: 10.1186-1753-6561-3-S4-S8

Cite this article as: Skarman, A., Jiang, L., Hornshøj, H. et al. BMC Proc 2009 3Suppl 4: S8. doi:10.1186-1753-6561-3-S4-S8


BackgroundGene 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.

ResultsApplying 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.

ConclusionBiological 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.

List of abbreviations usedGOGene Ontology

SVMSupport Vector Machine

FDRBenjamin and Hochberg-s False Discovery Rate

BPBiological Process

MFMolecular Function

CCCellular Component

Electronic supplementary materialThe online version of this article doi:10.1186-1753-6561-3-S4-S8 contains supplementary material, which is available to authorized users.

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Author: Axel Skarman - Li Jiang - Henrik Hornshøj - Bart Buitenhuis - Jakob Hedegaard - Lene N Conley - Peter Sørensen


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