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using ribosomal protein genes as reference a tale of caution使用核糖体蛋白基因作为引用一个谨慎的故事
Using Ribosomal Protein Genes as Reference: A Tale of
Caution
1,2,5 3,5 ´ 2,5 1,5
Lieven Thorrez , Katrijn Van Deun , Leon-Charles Tranchevent , Leentje Van Lommel , Kristof
Engelen4,5, Kathleen Marchal4,5, Yves Moreau2,5, Iven Van Mechelen3,5, Frans Schuit1,5*
1 Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium, 2 Department of Electrical Engineering, ESAT-SCD,
Katholieke Universiteit Leuven, Leuven, Belgium, 3 Department of Psychology, Katholieke Universiteit Leuven, Leuven, Belgium, 4 Department of Microbial and Molecular
Systems, Katholieke Universiteit Leuven, Leuven, Belgium, 5 SymBioSys, K.U.Leuven Center for Computational Systems Biology, Leuven, Belgium
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 visual
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