Using Ribosomal protein genes as reference: A tale of caution

Lieven Thorrez, K. Van Deun, Léon-charles Tranchevent, Leentje Van Lommel, Kristof Engelen, Kathleen Marchal, Yves Moreau, Iven Van Mechelen, Frans Schuit, Sui Huang (Editor)

Research output: Contribution to journalArticleScientificpeer-review

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.
Original languageEnglish
Article numbere1854
JournalPLoS ONE
Volume3
Issue number3
DOIs
Publication statusPublished - 2008
Externally publishedYes

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Ribosomal Proteins
Genes
Essential Genes
Tissue
Microarrays
Gene expression

Cite this

Thorrez, L., Van Deun, K., Tranchevent, L., Van Lommel, L., Engelen, K., Marchal, K., ... Huang, S. (Ed.) (2008). Using Ribosomal protein genes as reference: A tale of caution. PLoS ONE, 3(3), [e1854]. https://doi.org/10.1371/journal.pone.0001854
Thorrez, Lieven ; Van Deun, K. ; Tranchevent, Léon-charles ; Van Lommel, Leentje ; Engelen, Kristof ; Marchal, Kathleen ; Moreau, Yves ; Van Mechelen, Iven ; Schuit, Frans ; Huang, Sui (Editor). / Using Ribosomal protein genes as reference : A tale of caution. In: PLoS ONE. 2008 ; Vol. 3, No. 3.
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Thorrez, L, Van Deun, K, Tranchevent, L, Van Lommel, L, Engelen, K, Marchal, K, Moreau, Y, Van Mechelen, I, Schuit, F & Huang, S (ed.) 2008, 'Using Ribosomal protein genes as reference: A tale of caution', PLoS ONE, vol. 3, no. 3, e1854. https://doi.org/10.1371/journal.pone.0001854

Using Ribosomal protein genes as reference : A tale of caution. / Thorrez, Lieven; Van Deun, K.; Tranchevent, Léon-charles; Van Lommel, Leentje; Engelen, Kristof; Marchal, Kathleen; Moreau, Yves; Van Mechelen, Iven; Schuit, Frans; Huang, Sui (Editor).

In: PLoS ONE, Vol. 3, No. 3, e1854, 2008.

Research output: Contribution to journalArticleScientificpeer-review

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T2 - A tale of caution

AU - Thorrez, Lieven

AU - Van Deun, K.

AU - Tranchevent, Léon-charles

AU - Van Lommel, Leentje

AU - Engelen, Kristof

AU - Marchal, Kathleen

AU - Moreau, Yves

AU - Van Mechelen, Iven

AU - Schuit, Frans

A2 - Huang, Sui

PY - 2008

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N2 - BackgroundHousekeeping 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 FindingsWe 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/SignificanceHere 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.

AB - BackgroundHousekeeping 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 FindingsWe 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/SignificanceHere 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.

U2 - 10.1371/journal.pone.0001854

DO - 10.1371/journal.pone.0001854

M3 - Article

VL - 3

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 3

M1 - e1854

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Thorrez L, Van Deun K, Tranchevent L, Van Lommel L, Engelen K, Marchal K et al. Using Ribosomal protein genes as reference: A tale of caution. PLoS ONE. 2008;3(3). e1854. https://doi.org/10.1371/journal.pone.0001854