Candidate genes detected in transcriptome studies are strongly dependent on genetic background

Pernille Sarup, Jesper G. Sørensen, Torsten N. Kristensen, Ary A. Hoffmann, Volker Loeschcke, Ken N Paige, Peter Sørensen

Research output: Contribution to journalArticlepeer-review

Abstract

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds.

Original languageEnglish (US)
Article numbere15644
JournalPloS one
Volume6
Issue number1
DOIs
StatePublished - 2011

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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