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Open Access Highly Accessed Research article

A gene expression atlas of the domestic pig

Tom C Freeman1*, Alasdair Ivens26, J Kenneth Baillie1, Dario Beraldi17, Mark W Barnett1, David Dorward1, Alison Downing1, Lynsey Fairbairn1, Ronan Kapetanovic1, Sobia Raza1, Andru Tomoiu1, Ramiro Alberio3, Chunlei Wu4, Andrew I Su4, Kim M Summers1, Christopher K Tuggle5, Alan L Archibald1* and David A Hume1*

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK

2 Fios Genomics Ltd, ETTC, King's Buildings, Edinburgh EH9 3JL UK

3 Division of Animal Sciences, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD UK

4 Department of Molecular and Experimental Medicine, The Scripps Research Institute, MEM-216, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA

5 Department of Animal Science, Iowa State University, Ames, IA 50011, USA

6 Centre for Immunity, Infection and Evolution, University of Edinburgh Ashworth Labs, King's Buildings, West Mains Road, Edinburgh EH9 3JT

7 Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson way, Cambridge, CB2 0RE, UK

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BMC Biology 2012, 10:90  doi:10.1186/1741-7007-10-90

Published: 15 November 2012

Abstract

Background

This work describes the first genome-wide analysis of the transcriptional landscape of the pig. A new porcine Affymetrix expression array was designed in order to provide comprehensive coverage of the known pig transcriptome. The new array was used to generate a genome-wide expression atlas of pig tissues derived from 62 tissue/cell types. These data were subjected to network correlation analysis and clustering.

Results

The analysis presented here provides a detailed functional clustering of the pig transcriptome where transcripts are grouped according to their expression pattern, so one can infer the function of an uncharacterized gene from the company it keeps and the locations in which it is expressed. We describe the overall transcriptional signatures present in the tissue atlas, where possible assigning those signatures to specific cell populations or pathways. In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human. We identify sets of genes that define specialized cellular compartments and region-specific digestive functions. Finally, we performed a network analysis of the transcription factors expressed in the gastrointestinal tract and demonstrate how they sub-divide into functional groups that may control cellular gastrointestinal development.

Conclusions

As an important livestock animal with a physiology that is more similar than mouse to man, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells. The data and analyses are available on the websites http://biogps.org and http://www.macrophages.com/pig-atlas webcite.

Keywords:
pig; porcine; Sus scrofa; microarray; transcriptome; transcription network; pathway; gastrointestinal tract