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

Additional files

Additional file 1:

Table S1. Details of the tissues and cells used for this study. List and details of tissues and cells used for this study.

Format: XLSX Size: 15KB Download file

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Additional file 2:

Pig atlas '.expression' file. File of all RMA normalized data describing the expression pattern of the majority of porcine genes across 63 tissue/cell types. File may be opened in Microsoft Excel or BioLayout Express3D.

Format: EXPRESSION Size: 22.6MB Download file

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Additional file 3:

Pig atlas network '.layout' file. Precalculated network layout of the graph used in this analysis. The network contains 20,355 nodes (probesets) and 1,251,575 edges (correlations ≥0.8) that can be visualized in BioLayout Express3D (http://www.biolayout.org). This is a large graph and requires good hardware (a decent graphics card and sufficient RAM) to render and navigate. See http://www.biolayout.org/download/requirements/ webcite for the requirements to run this program.

Format: LAYOUT Size: 81.8MB Download file

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Additional file 4:

Table S2. Fully annotated cluster analysis (r > 0.8, MCL inflation 2.2) of the pig expression atlas network. The gene/transcript membership of each cluster is defined together with a description of the average expression profile of each of the major clusters and known association of the genes with a tissue, cell type or pathway.

Format: XLSX Size: 4.5MB Download file

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Additional file 5:

Figure S1. Expression profiles of selected gene family members/functionally related genes along the length of the GI tract. A number of gene families were selected and the profile of specific members investigated. A. The keratins are a large gene family where the expression of individual members is associated with specific classes of epithelial/dermal layers. In this case there are numerous family members expressed in the stratified squamous epithelia of the tongue and esophagus whereas others are expressed specifically in columnar epithelia of the mid to lower GI tract. B. Expression of digestive enzymes is in most cases restricted to the small intestinal enterocytes but individual patterns of expression along the longitudinal axis of the region do vary in line with requirements. C. In common with the genes shown in B, expression of the solute transporters associated with absorption mirrors the requirement for their activity being expressed in a region-specific manner along the small and large intestine. D. Mucins play a crucial role in the lubrication and protection of the GI tract. The profiles of a number of gene family members are shown, some of which are highly expressed in the salivary gland (MUC12, MUC19), others in the stomach (MUC1, MUC5AC) and MUC4's expression is restricted to the colon. E. Regulating many aspects of GI function are a range of hormones expressed by endocrine cells that line the organ. The expression of the hormone genes shown here is largely restricted to the stomach and duodenum. F. Expression of T and B cell marker genes whose expression peaks in the ileum where the immune cell content of the organ is at its highest. G. Myosins are essential components of muscle fibers and are utilized differently in different types of muscle. In this case they segregate according to the distribution of skeletal muscle (tongue, esophagus) or smooth muscle (other regions). H. Many collagens are required for the formation of the extracellular matrix that is a major component of connective tissues and is produced by various mesenchymal cells types particularly fibroblasts. These genes are consequently observed to be expressed along the entire GI tract albeit in a region-dependent manner.

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Additional file 6:

Figure S2. Screenshots of the GI tract transcriptional network in 2D and 3D. Visualization of the transcriptional network associated with the pig GI tract. The network contains 5,199 nodes (probesets) connected by 195,272 edges (transcript-to-transcript correlations above 0.9); node color represents cluster membership. The same graph rendered in a two dimensional plane (inset).

Format: PDF Size: 13.1MB Download file

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Additional file 7:

Pig GI tract '.expression' file. File of all RMA normalized data describing the expression pattern of a subset of porcine genes across 15 regions of the porcine GI tract. File may be opened in Microsoft Excel or BioLayout Express3D.

Format: EXPRESSION Size: 2MB Download file

Open Data

Additional file 8:

Pig GI tract network '.layout' file. Precalculated network layout of the graph used in this analysis. The network contains 5,199 nodes (probesets) 195,272 edges (correlations ≥0.9) that can be visualized in BioLayout Express3D.

Format: LAYOUT Size: 16.7MB Download file

Open Data

Additional file 9:

Table S3. Fully annotated cluster analysis (r > 0.9, MCL inflation 1.7) of the pig gastrointestinal tract expression network. The gene/transcript membership of each cluster is defined together with a description of the average expression profile of each of the major clusters and known association of the genes with a tissue, cell type or pathway.

Format: XLSX Size: 666KB Download file

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Additional file 10:

Figure S3. Sample-to-sample Pearson correlation graph. A sample-to-sample Pearson correlation was calculated and relationships r > 0.91 used to group samples together. Nodes represent different samples and the edges relationships above the cutoff, the thicker/redder the line the greater the similarity between samples. The graph has been clustered using an MCL inflation value of 6.

Format: PDF Size: 1.3MB Download file

This file can be viewed with: Adobe Acrobat Reader

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