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. 2007 Sep 19;2(9):e898.
doi: 10.1371/journal.pone.0000898.

Evidence based selection of housekeeping genes

Hendrik J M de Jonge  1 , 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
Affiliations

Evidence based selection of housekeeping genes

Hendrik J M de Jonge et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Expression distribution of the top 15 candidate housekeeping genes (A) and of 12 commonly used housekeeping genes in 13,629 human samples (B).
Figure 2
Figure 2. PCR results of 5 novel candidate housekeeping genes.
S indicates sample, cDNA of a HL-60 leukemic cell line was used for all primers, B indicates the blanc (H2O) and L indicates the 100 base pair ladder (Fermentas).
See this image and copyright information in PMC

References

    1. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000;25:169–193. - PubMed
    1. Chuaqui RF, Bonner RF, Best CJ, Gillespie JW, Flaig MJ, et al. Post-analysis follow-up and validation of microarray experiments. Nat Genet. 2002;(32 Suppl):509–514. - PubMed
    1. Fink L, Seeger W, Ermert L, Hanze J, Stahl U, et al. Real-time quantitative RT-PCR after laser-assisted cell picking. Nat Med. 1998;4:1329–1333. - PubMed
    1. Giulietti A, Overbergh L, Valckx D, Decallonne B, Bouillon R, et al. An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods. 2001;25:386–401. - PubMed
    1. Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996;6:986–994. - PubMed

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