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A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA - BMC Biol. (2012)

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

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Collapsed cluster diagram of porcine GI tract expression network together withthe average gene profile of transcripts within selected clusters. A.Collapsed cluster diagram shown here is a simplified view of the graph used forthe analysis of the GI tract [see Additional file 6,Figure S2 for screenshot of transcript level graph]. Each node represents acluster of genes, the size of the node being proportional to the number ofindividual nodes (probesets) with that cluster. Edges represent connectionsbetween clusters whereby nodes in one cluster share edges with nodes in another.The color of the nodes has been selected to represent clusters of genes expressedin similar tissue types. B. Block diagrams of the average gene expressionprofile of the major GI clusters. Expression levels are indicated as a % ofmaximum with values rounded to the nearest 10%, each GI compartment analyzed beingrepresented as a separate block. A key to the size of each block is shown in thebottom right hand corner. Gene clusters have been grouped according to cell typeof origin: purple, stratified squamous epithelia; brown, salivary stratifiedcolumnar epithelia; light green, ciliated/glandular columnar epithelia; darkgreen, immune cells/cell cycle; blue, musculature (smooth and skeletal); grey,neuronal. GI, gastrointestinal.
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Figure 5: Collapsed cluster diagram of porcine GI tract expression network together withthe average gene profile of transcripts within selected clusters. A.Collapsed cluster diagram shown here is a simplified view of the graph used forthe analysis of the GI tract [see Additional file 6,Figure S2 for screenshot of transcript level graph]. Each node represents acluster of genes, the size of the node being proportional to the number ofindividual nodes (probesets) with that cluster. Edges represent connectionsbetween clusters whereby nodes in one cluster share edges with nodes in another.The color of the nodes has been selected to represent clusters of genes expressedin similar tissue types. B. Block diagrams of the average gene expressionprofile of the major GI clusters. Expression levels are indicated as a % ofmaximum with values rounded to the nearest 10%, each GI compartment analyzed beingrepresented as a separate block. A key to the size of each block is shown in thebottom right hand corner. Gene clusters have been grouped according to cell typeof origin: purple, stratified squamous epithelia; brown, salivary stratifiedcolumnar epithelia; light green, ciliated/glandular columnar epithelia; darkgreen, immune cells/cell cycle; blue, musculature (smooth and skeletal); grey,neuronal. GI, gastrointestinal.

Mentions: The GI tract data were prefiltered to remove low intensity signals and technicalartefacts, and the remaining data (from 5,199 probesets) subjected to network analysis.A collapsed cluster diagram of the network is shown in Figure 5aand screenshots of the transcript level network in Additional file 6, Figure S2. Annotated '.expression' and '.layout' files are given inAdditional files 7 and 8,respectively. The data divided into 120 clusters of coexpressed genes (Figure 5b). A listing of the main clusters and an interpretation of the genesignatures is shown in Table 4 and a full listing of the geneswithin those clusters is provided in Additional file 9, TableS3.


A gene expression atlas of the domestic pig.

Freeman TC, Ivens A, Baillie JK, Beraldi D, Barnett MW, Dorward D, Downing A, Fairbairn L, Kapetanovic R, Raza S, Tomoiu A, Alberio R, Wu C, Su AI, Summers KM, Tuggle CK, Archibald AL, Hume DA - BMC Biol. (2012)

Collapsed cluster diagram of porcine GI tract expression network together withthe average gene profile of transcripts within selected clusters. A.Collapsed cluster diagram shown here is a simplified view of the graph used forthe analysis of the GI tract [see Additional file 6,Figure S2 for screenshot of transcript level graph]. Each node represents acluster of genes, the size of the node being proportional to the number ofindividual nodes (probesets) with that cluster. Edges represent connectionsbetween clusters whereby nodes in one cluster share edges with nodes in another.The color of the nodes has been selected to represent clusters of genes expressedin similar tissue types. B. Block diagrams of the average gene expressionprofile of the major GI clusters. Expression levels are indicated as a % ofmaximum with values rounded to the nearest 10%, each GI compartment analyzed beingrepresented as a separate block. A key to the size of each block is shown in thebottom right hand corner. Gene clusters have been grouped according to cell typeof origin: purple, stratified squamous epithelia; brown, salivary stratifiedcolumnar epithelia; light green, ciliated/glandular columnar epithelia; darkgreen, immune cells/cell cycle; blue, musculature (smooth and skeletal); grey,neuronal. GI, gastrointestinal.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814290&req=5

Figure 5: Collapsed cluster diagram of porcine GI tract expression network together withthe average gene profile of transcripts within selected clusters. A.Collapsed cluster diagram shown here is a simplified view of the graph used forthe analysis of the GI tract [see Additional file 6,Figure S2 for screenshot of transcript level graph]. Each node represents acluster of genes, the size of the node being proportional to the number ofindividual nodes (probesets) with that cluster. Edges represent connectionsbetween clusters whereby nodes in one cluster share edges with nodes in another.The color of the nodes has been selected to represent clusters of genes expressedin similar tissue types. B. Block diagrams of the average gene expressionprofile of the major GI clusters. Expression levels are indicated as a % ofmaximum with values rounded to the nearest 10%, each GI compartment analyzed beingrepresented as a separate block. A key to the size of each block is shown in thebottom right hand corner. Gene clusters have been grouped according to cell typeof origin: purple, stratified squamous epithelia; brown, salivary stratifiedcolumnar epithelia; light green, ciliated/glandular columnar epithelia; darkgreen, immune cells/cell cycle; blue, musculature (smooth and skeletal); grey,neuronal. GI, gastrointestinal.
Mentions: The GI tract data were prefiltered to remove low intensity signals and technicalartefacts, and the remaining data (from 5,199 probesets) subjected to network analysis.A collapsed cluster diagram of the network is shown in Figure 5aand screenshots of the transcript level network in Additional file 6, Figure S2. Annotated '.expression' and '.layout' files are given inAdditional files 7 and 8,respectively. The data divided into 120 clusters of coexpressed genes (Figure 5b). A listing of the main clusters and an interpretation of the genesignatures is shown in Table 4 and a full listing of the geneswithin those clusters is provided in Additional file 9, TableS3.

Bottom Line: 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.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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH
Related in: MedlinePlus