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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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Network topology of porcine expression atlas. The collapsed cluster diagramshown here is a simplified view of the graph used for this analysis and shown inFigure 1. Each node represents one of the 150 largest clusters of genes, the sizeof the node being proportional to the number of individual nodes (probesets)within that cluster. Edges represent connections between clusters whereby nodes inone cluster share edges with nodes in another. The color of the nodes has beenselected to represent clusters of genes expressed in given types of tissues whichtend to group together with the overall topology of the network.
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Figure 2: Network topology of porcine expression atlas. The collapsed cluster diagramshown here is a simplified view of the graph used for this analysis and shown inFigure 1. Each node represents one of the 150 largest clusters of genes, the sizeof the node being proportional to the number of individual nodes (probesets)within that cluster. Edges represent connections between clusters whereby nodes inone cluster share edges with nodes in another. The color of the nodes has beenselected to represent clusters of genes expressed in given types of tissues whichtend to group together with the overall topology of the network.

Mentions: We used BioLayout Express3D to analyze the pig transcriptome datagenerated using the Snowball array (all normalized expression data is provided inAdditional file 2). From a pairwise transcript-to-transcriptcorrelation matrix a weighted, undirected network graph was constructed using a Pearsoncorrelation threshold cut-off of r ≥ 0.80. The resultant graph was large andhighly structured (Figure 1, Additional file 3) with one large component of 19,708 nodes and 90 smaller components(unconnected networks of correlations) of between 57 and 5 nodes (20,352 probesets intotal, that is, just under half the transcripts represented on the array). The topologyof the graph contained localized areas of high connectivity and high correlation(representing groups of genes with similar profiles), dominated by groups of genes thatare coexpressed and form highly connected cliques within the network (Figures 1 and 2). Nodes representing differentprobesets designed to the same gene were generally highly correlated and connected toeach other in the graph, confirming the validity of the probeset annotation andapproach.


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)

Network topology of porcine expression atlas. The collapsed cluster diagramshown here is a simplified view of the graph used for this analysis and shown inFigure 1. Each node represents one of the 150 largest clusters of genes, the sizeof the node being proportional to the number of individual nodes (probesets)within that cluster. Edges represent connections between clusters whereby nodes inone cluster share edges with nodes in another. The color of the nodes has beenselected to represent clusters of genes expressed in given types of tissues whichtend to group together with the overall topology of the network.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Network topology of porcine expression atlas. The collapsed cluster diagramshown here is a simplified view of the graph used for this analysis and shown inFigure 1. Each node represents one of the 150 largest clusters of genes, the sizeof the node being proportional to the number of individual nodes (probesets)within that cluster. Edges represent connections between clusters whereby nodes inone cluster share edges with nodes in another. The color of the nodes has beenselected to represent clusters of genes expressed in given types of tissues whichtend to group together with the overall topology of the network.
Mentions: We used BioLayout Express3D to analyze the pig transcriptome datagenerated using the Snowball array (all normalized expression data is provided inAdditional file 2). From a pairwise transcript-to-transcriptcorrelation matrix a weighted, undirected network graph was constructed using a Pearsoncorrelation threshold cut-off of r ≥ 0.80. The resultant graph was large andhighly structured (Figure 1, Additional file 3) with one large component of 19,708 nodes and 90 smaller components(unconnected networks of correlations) of between 57 and 5 nodes (20,352 probesets intotal, that is, just under half the transcripts represented on the array). The topologyof the graph contained localized areas of high connectivity and high correlation(representing groups of genes with similar profiles), dominated by groups of genes thatare coexpressed and form highly connected cliques within the network (Figures 1 and 2). Nodes representing differentprobesets designed to the same gene were generally highly correlated and connected toeach other in the graph, confirming the validity of the probeset annotation andapproach.

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