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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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Screenshot of the representation of the profile of the pig A2M genewithin the BioGPS online portal. All data used for this study are availablethrough the BioGPS database. Genes can be searched for and where found the fullexpression profile is displayed as a bar chart. Samples are colored according totype, for example, CNS, GI tract, and so on, and the interface supports a numberof useful features including a zoom function on the profile viewer, searches forgenes with a similar profile, access to the raw data, links to external resourcesand the potential to compare profiles across species, for example, human, mouse,rat, zebrafish, frog. CNS, central nervous system; GI, gastrointestinal.
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Figure 3: Screenshot of the representation of the profile of the pig A2M genewithin the BioGPS online portal. All data used for this study are availablethrough the BioGPS database. Genes can be searched for and where found the fullexpression profile is displayed as a bar chart. Samples are colored according totype, for example, CNS, GI tract, and so on, and the interface supports a numberof useful features including a zoom function on the profile viewer, searches forgenes with a similar profile, access to the raw data, links to external resourcesand the potential to compare profiles across species, for example, human, mouse,rat, zebrafish, frog. CNS, central nervous system; GI, gastrointestinal.

Mentions: Some highly expressed genes were not included in the graph. The more unique a gene'sexpression pattern, the fewer neighbors it will have in the network. One example is theprotease inhibitor, alpha-2-macroglobulin (A2M). There were five probesets onthe array designed to this gene and all showed a highly similar expression pattern,albeit at a range of signal intensities. These probesets formed a small correlationnetwork with themselves, but the expression pattern of this gene in the context of thefull atlas was essentially unique and no other porcine gene was expressed in this manner(Figure 3). In some cases, such isolation is a consequence of theuse of distinct cell-restricted promoters [10,32]. For A2M, there is a single major transcription start site in bothmouse and human, and the pattern of expression is similar in these two species ([10]http://biogps.org) and in pig, suggesting that a common set ofregulatory factors control this gene's expression across species. For the majority ofother probesets not found in the graph described here, transcripts appear to beexpressed at very low levels (or not at all). These genes may be highly-expressed incells or tissues we have not sampled in this sample set. For example, we would notdetect genes exclusively expressed during prenatal life as no samples from these stageswere represented in the current atlas.


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)

Screenshot of the representation of the profile of the pig A2M genewithin the BioGPS online portal. All data used for this study are availablethrough the BioGPS database. Genes can be searched for and where found the fullexpression profile is displayed as a bar chart. Samples are colored according totype, for example, CNS, GI tract, and so on, and the interface supports a numberof useful features including a zoom function on the profile viewer, searches forgenes with a similar profile, access to the raw data, links to external resourcesand the potential to compare profiles across species, for example, human, mouse,rat, zebrafish, frog. CNS, central nervous system; GI, gastrointestinal.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Screenshot of the representation of the profile of the pig A2M genewithin the BioGPS online portal. All data used for this study are availablethrough the BioGPS database. Genes can be searched for and where found the fullexpression profile is displayed as a bar chart. Samples are colored according totype, for example, CNS, GI tract, and so on, and the interface supports a numberof useful features including a zoom function on the profile viewer, searches forgenes with a similar profile, access to the raw data, links to external resourcesand the potential to compare profiles across species, for example, human, mouse,rat, zebrafish, frog. CNS, central nervous system; GI, gastrointestinal.
Mentions: Some highly expressed genes were not included in the graph. The more unique a gene'sexpression pattern, the fewer neighbors it will have in the network. One example is theprotease inhibitor, alpha-2-macroglobulin (A2M). There were five probesets onthe array designed to this gene and all showed a highly similar expression pattern,albeit at a range of signal intensities. These probesets formed a small correlationnetwork with themselves, but the expression pattern of this gene in the context of thefull atlas was essentially unique and no other porcine gene was expressed in this manner(Figure 3). In some cases, such isolation is a consequence of theuse of distinct cell-restricted promoters [10,32]. For A2M, there is a single major transcription start site in bothmouse and human, and the pattern of expression is similar in these two species ([10]http://biogps.org) and in pig, suggesting that a common set ofregulatory factors control this gene's expression across species. For the majority ofother probesets not found in the graph described here, transcripts appear to beexpressed at very low levels (or not at all). These genes may be highly-expressed incells or tissues we have not sampled in this sample set. For example, we would notdetect genes exclusively expressed during prenatal life as no samples from these stageswere represented in the current atlas.

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