title: A gene expression atlas of the domestic pig.
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.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9PS, UK. tom.freeman@roslin.ed.ac.uk
authors.forename: Tom C
authors.initials: TC
authors.lastname: Freeman
authors.forename: Alasdair
authors.initials: A
authors.lastname: Ivens
authors.forename: J Kenneth
authors.initials: JK
authors.lastname: Baillie
authors.forename: Dario
authors.initials: D
authors.lastname: Beraldi
authors.forename: Mark W
authors.initials: MW
authors.lastname: Barnett
authors.forename: David
authors.initials: D
authors.lastname: Dorward
authors.forename: Alison
authors.initials: A
authors.lastname: Downing
authors.forename: Lynsey
authors.initials: L
authors.lastname: Fairbairn
authors.forename: Ronan
authors.initials: R
authors.lastname: Kapetanovic
authors.forename: Sobia
authors.initials: S
authors.lastname: Raza
authors.forename: Andru
authors.initials: A
authors.lastname: Tomoiu
authors.forename: Ramiro
authors.initials: R
authors.lastname: Alberio
authors.forename: Chunlei
authors.initials: C
authors.lastname: Wu
authors.forename: Andrew I
authors.initials: AI
authors.lastname: Su
authors.forename: Kim M
authors.initials: KM
authors.lastname: Summers
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Tuggle
authors.forename: Alan L
authors.initials: AL
authors.lastname: Archibald
authors.forename: David A
authors.initials: DA
authors.lastname: Hume
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D016678:Genome; D009928:Organ Specificity; D013552:Swine / Q000235:genetics*; D059467:Transcriptome