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Evidence Based Selection of Housekeeping Genes

Author

Listed:
  • Hendrik J M de Jonge
  • Rudolf S N Fehrmann
  • Eveline S J M de Bont
  • Robert M W Hofstra
  • Frans Gerbens
  • Willem A Kamps
  • Elisabeth G E de Vries
  • Ate G J van der Zee
  • Gerard J te Meerman
  • Arja ter Elst

Abstract

For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes (reference or internal control genes) is required. It is known that commonly used housekeeping genes (e.g. ACTB, GAPDH, HPRT1, and B2M) vary considerably under different experimental conditions and therefore their use for normalization is limited. We performed a meta-analysis of 13,629 human gene array samples in order to identify the most stable expressed genes. Here we show novel candidate housekeeping genes (e.g. RPS13, RPL27, RPS20 and OAZ1) with enhanced stability among a multitude of different cell types and varying experimental conditions. None of the commonly used housekeeping genes were present in the top 50 of the most stable expressed genes. In addition, using 2,543 diverse mouse gene array samples we were able to confirm the enhanced stability of the candidate novel housekeeping genes in another mammalian species. Therefore, the identified novel candidate housekeeping genes seem to be the most appropriate choice for normalizing gene expression data.

Suggested Citation

  • Hendrik J M de Jonge & Rudolf S N Fehrmann & Eveline S J M de Bont & Robert M W Hofstra & Frans Gerbens & Willem A Kamps & Elisabeth G E de Vries & Ate G J van der Zee & Gerard J te Meerman & Arja ter, 2007. "Evidence Based Selection of Housekeeping Genes," PLOS ONE, Public Library of Science, vol. 2(9), pages 1-5, September.
    • Handle: RePEc:plo:pone00:0000898
    DOI: 10.1371/journal.pone.0000898
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    Cited by:

    1. Lieven Thorrez & Katrijn Van Deun & Léon-Charles Tranchevent & Leentje Van Lommel & Kristof Engelen & Kathleen Marchal & Yves Moreau & Iven Van Mechelen & Frans Schuit, 2008. "Using Ribosomal Protein Genes as Reference: A Tale of Caution," PLOS ONE, Public Library of Science, vol. 3(3), pages 1-8, March.
    2. Florian R L Meyer & Heinrich Grausgruber & Claudia Binter & Georg E Mair & Christian Guelly & Claus Vogl & Ralf Steinborn, 2013. "Cross-Platform Microarray Meta-Analysis for the Mouse Jejunum Selects Novel Reference Genes with Highly Uniform Levels of Expression," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-15, May.
    3. Yijuan Zhang & Ding Li & Bingyun Sun, 2015. "Do Housekeeping Genes Exist?," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-22, May.
    4. Wei-Chung Cheng & Cheng-Wei Chang & Chaang-Ray Chen & Min-Lung Tsai & Wun-Yi Shu & Chia-Yang Li & Ian C Hsu, 2011. "Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis," PLOS ONE, Public Library of Science, vol. 6(2), pages 1-8, February.
    5. Bo Dong & Peng Zhang & Xiaowei Chen & Li Liu & Yunfei Wang & Shunmin He & Runsheng Chen, 2011. "Predicting Housekeeping Genes Based on Fourier Analysis," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-11, June.

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