A Gene Expression Atlas of the Domestic Pig

From: Tom C. Freeman, Alasdair Ivens, J. Kenneth Baillie, Dario Beraldi, Mark Barnett, David Dorward, Alison Downing, Lynsey Fairbairn, Ronan Kapetanovic, Sobia Raza, Andru Tomoiu, Ramiro Alberio, Kim M. Summers, Christopher K. Tuggle, Alan L. Archibald and David A. Hume, 2012

This work describes the first genome-wide analysis of the transcriptional landscape of the pig.  As an important livestock animal with a physiology that is more similar to man than mouse, we provide a major new resource for understanding gene expression with respect to the known physiology of mammalian tissues and cells.  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 (including macrophages). 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 uncharacterised 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 specialised 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. The data and analyses are available here on www.macrophages.com (see below) and http://www.biogps.org.

Gene Expression Network Analysis

BioLayout Filesets 1: Following QC, data from 104 arrays run on samples derived from 62 tissue/cell types were normalised using the robust multi-array average (RMA) expression measure. Taking the normalised untransformed expression data a pairwise Pearson correlation matrix was calculated for each probeset on the array as a measure of similarity between the signal derived from different probesets. A correlation cut off of r = 0.8 was used to construct a graph containing 20,355 nodes (probesets) and 1,251,575 edges. Gene coexpression clusters were determined using MCL clustering algorithm, at an inflation value of 2.2. Clusters are annotated according to size and known gene function shared by multiple members of a cluster.

Warning: BioLayout Fileset 1 renders a very large graph (>20,000 nodes); before launching this BioLayout webstart please ensure your machine meets the minimum hardware specifications for displaying large graphs; please see: http://www.biolayout.org/download/requirements/ 

BioLayout Filesets 2: In order to focus down specifically on expression patterns along the porcine gastrointestinal (GI) tract, the data from these tissues (30 samples in total) were treated separately.  Data were removed for all probesets where the maximum normalized expression value never exceeded a value of 50 in any of the GI samples.  This filtering left 29,918 probesets.  These data were then subjected to network analysis at a correlation cut-off value of r = 0.90 and clustered using an MCL inflation value of 2.2.  This network was inspected manually and clusters were removed where they showed no particular region-specific expression pattern or were most likely formed due to contamination of gastrointestinal tissues with surrounding tissues.The remaining data were again subjected to network analysis (r = 0.90) producing a graph composed of 5,199 nodes/195,272 edges which was clustered using an MCL inflation value of 1.7. The resulting cluster analysis of 120 clusters, was then explored in order to annotate the most likely cellular source of the expression signatures observed.

ArrayExpress ID: E-MTAB-1183

Gene expression analysis across 62 tissue/cell types derived from the pig.
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Expression profiling by array
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