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Title: Using Ribosomal Protein genes as reference: a tale of caution
Authors: Thorrez, Lieven ×
Van Deun, Katrijn
Tranchevent, Léon-Charles
Van Lommel, Leentje
Engelen, Kristof
Marchal, Kathleen
Moreau, Yves
Van Mechelen, Iven
Schuit, Frans #
Issue Date: Mar-2008
Publisher: Public Library of Sciene
Series Title: PLoS One vol:3 issue:3 pages:e1854
Abstract: BACKGROUND: Housekeeping genes are needed in every tissue as their expression is required for survival, integrity or duplication of every cell. Housekeeping genes commonly have been used as reference genes to normalize gene expression data, the underlying assumption being that they are expressed in every cell type at approximately the same level. Often, the terms "reference genes" and "housekeeping genes" are used interchangeably. In this paper, we would like to distinguish between these terms. Consensus is growing that housekeeping genes which have traditionally been used to normalize gene expression data are not good reference genes. Recently, ribosomal protein genes have been suggested as reference genes based on a meta-analysis of publicly available microarray data. METHODOLOGY/PRINCIPAL FINDINGS: We have applied several statistical tools on a dataset of 70 microarrays representing 22 different tissues, to assess and visualize expression stability of ribosomal protein genes. We confirmed the housekeeping status of these genes, but further estimated expression stability across tissues in order to assess their potential as reference genes. One- and two-way ANOVA revealed that all ribosomal protein genes have significant expression variation across tissues and exhibit tissue-dependent expression behavior as a group. Via multidimensional unfolding analysis, we visualized this tissue-dependency. In addition, we explored mechanisms that may cause tissue dependent effects of individual ribosomal protein genes. CONCLUSIONS/SIGNIFICANCE: Here we provide statistical and biological evidence that ribosomal protein genes exhibit important tissue-dependent variation in mRNA expression. Though these genes are most stably expressed of all investigated genes in a meta-analysis they cannot be considered true reference genes.
URI: 
ISSN: 1932-6203
Publication status: published
KU Leuven publication type: IT
Appears in Collections:ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Quantitative Psychology and Individual Differences
Centre of Microbial and Plant Genetics
Biochemistry Section (Medicine) (-)
Gene Expression Unit
× corresponding author
# (joint) last author

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