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A novel method for ...
A novel method for cross-species gene expression analysis
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- Kristiansson, Erik, 1978 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
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- Österlund, Tobias, 1984 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Gunnarsson, Lina-Maria, 1977 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för neurovetenskap och fysiologi, sektionen för fysiologi,Institute of Neuroscience and Physiology, Department of Physiology,University of Gothenburg
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- Arne, Gabriella (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för patologi,Institute of Biomedicine, Department of Pathology,University of Gothenburg
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- Larsson, D. G. Joakim, 1969 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för biomedicin, avdelningen för infektionssjukdomar,Institute of Biomedicine, Department of Infectious Medicine,University of Gothenburg
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- Nerman, Olle, 1951 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Department of Mathematical Sciences, Mathematical Statistics,University of Gothenburg,Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- 2013-02-27
- 2013
- Engelska.
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 14
- Relaterad länk:
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https://gup.ub.gu.se... (primary) (free)
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https://bmcbioinform...
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http://publications.... (primary) (free)
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Background Analysis of gene expression from different species is a powerful way to identify evolutionarily conserved transcriptional responses. However, due to evolutionary events such as gene duplication, there is no one-to-one correspondence between genes from different species which makes comparison of their expression profiles complex. Results In this paper we describe a new method for cross-species meta-analysis of gene expression. The method takes the homology structure between compared species into account and can therefore compare expression data from genes with any number of orthologs and paralogs. A simulation study shows that the proposed method results in a substantial increase in statistical power compared to previously suggested procedures. As a proof of concept, we analyzed microarray data from heat stress experiments performed in eight species and identified several well-known evolutionarily conserved transcriptional responses. The method was also applied to gene expression profiles from five studies of estrogen exposed fish and both known and potentially novel responses were identified. Conclusions The method described in this paper will further increase the potential and reliability of meta-analysis of gene expression profiles from evolutionarily distant species. The method has been implemented in R and is freely available at http://bioinformatics.math.chalmers.se/Xspecies/ webcite.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Annan medicin och hälsovetenskap (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Other Medical and Health Sciences (hsv//eng)
Nyckelord
- Gene expression
- Evolution
- Meta-analysis
- Orthologs
- Paralogs
- Microarray
- RNA-seq
- Microarray
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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