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

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 i...

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Autores principales:	Pernille Sarup, Jesper G Sørensen, Torsten N Kristensen, Ary A Hoffmann, Volker Loeschcke, Ken N Paige, Peter Sørensen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/04e651eec91f4fccba271d9b4b4a5b50
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id	oai:doaj.org-article:04e651eec91f4fccba271d9b4b4a5b50
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spelling	oai:doaj.org-article:04e651eec91f4fccba271d9b4b4a5b502021-11-18T06:59:55ZCandidate genes detected in transcriptome studies are strongly dependent on genetic background.1932-620310.1371/journal.pone.0015644https://doaj.org/article/04e651eec91f4fccba271d9b4b4a5b502011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21283582/?tool=EBIhttps://doaj.org/toc/1932-6203Whole 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.Pernille SarupJesper G SørensenTorsten N KristensenAry A HoffmannVolker LoeschckeKen N PaigePeter SørensenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 1, p e15644 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pernille Sarup Jesper G Sørensen Torsten N Kristensen Ary A Hoffmann Volker Loeschcke Ken N Paige Peter Sørensen Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
description	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.
format	article
author	Pernille Sarup Jesper G Sørensen Torsten N Kristensen Ary A Hoffmann Volker Loeschcke Ken N Paige Peter Sørensen
author_facet	Pernille Sarup Jesper G Sørensen Torsten N Kristensen Ary A Hoffmann Volker Loeschcke Ken N Paige Peter Sørensen
author_sort	Pernille Sarup
title	Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
title_short	Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
title_full	Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
title_fullStr	Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
title_full_unstemmed	Candidate genes detected in transcriptome studies are strongly dependent on genetic background.
title_sort	candidate genes detected in transcriptome studies are strongly dependent on genetic background.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/04e651eec91f4fccba271d9b4b4a5b50
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Candidate genes detected in transcriptome studies are strongly dependent on genetic background.

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