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Effects of threshold choice on the results of gene expression profiling, using microarray analysis, in a model feeding experiment with rat
Research Group Functional Genomics.
Research Unit Genetics and Biometrics.
Research Unit Genetics and Biometrics.ORCID iD: 0000-0002-7173-5579
Institute of Veterinary Anatomy, Department of Veterinary Medicine, Free University of Berlin, Berlin, Germany.
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2009 (English)In: Archiv für Tierzucht, ISSN 0003-9438, Vol. 52, no 1, 65-78 p.Article in journal (Refereed) Published
Abstract [en]

Global gene expression studies using microarray technology are widely employed to identify biological processes which are influenced by a treatment e.g. a specific diet. Affected processes are characterized by a significant enrichment of differentially expressed genes (functional annotation analysis). However, different choices of statistical thresholds to select candidates for differential expression will alter the resulting candidates list. This study was conducted to investigate the effect of applying a False Discovery Rate (FDR) correction and different fold change thresholds in statistical analysis of microarray data on diet-affected biological processes based on a significantly increased proportion of differentially expressed genes. In a model feeding experiment with rats fed genetically modified food additives, animals received a supplement of either lyophilized inactivated recombinant VP60 baculovirus (rBV-VP60) or lyophilized inactivated wild type baculovirus (wtBV). Comparative expression profiling was done in spleen, liver and small intestine mucosa. We demonstrated the extent to which threshold choice can affect the biological processes identified as significantly regulated and thus the conclusion drawn from the microarray data. In our study, the combined application of a moderate fold change threshold (FC≥1.5) and a stringent FDR threshold (q≤0.05) exhibited high reliability of biological processes identified as differentially regulated. The application of a stringent FDR threshold of q≤0.05 seems to be an essential prerequisite to reduce considerably the number of false positives. Microarray results of selected differentially expressed molecules were validated successfully by using real-time RT-PCR.

Place, publisher, year, edition, pages
Dummerstorf, Germany: Research Institute for the Biology of Farm Animals (FBN) , 2009. Vol. 52, no 1, 65-78 p.
Keyword [en]
Biological process; False discovery rate; Fold change threshold; Microarray expression profiling
National Category
Bioinformatics and Systems Biology
URN: urn:nbn:se:oru:diva-40733ISI: 000263312600008ScopusID: 2-s2.0-61649098016OAI: diva2:778566
Available from: 2015-01-11 Created: 2015-01-11 Last updated: 2015-06-03Bibliographically approved

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Repsilber, Dirk
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