Abstract
BackgroundGene expression microarrays have been intensively applied to screen for genes involved in specific biological processes of interest such as diseases or responses to environmental stimuli. For mammalian species, cataloging of the global gene expression profiles in large tissue collections under normal conditions have been focusing on human and mouse genomes but is lacking for the pig genome.Methodology/Principal FindingsHere we present the results from a large-scale porcine study establishing microarray cDNA expression profiles of approximately 20.000 genes across 23 healthy tissues. As expected, a large portion of the genes show tissue specific expression in agreement with mappings to gene descriptions, Gene Ontology terms and KEGG pathways. Two-way hierarchical clustering identified expected tissue clusters in accordance with tissue type and a number of cDNA clusters having similar gene expression patterns across tissues. For one of these cDNA clusters, we demonstrate that possible tissue associated gene function can be inferred for previously uncharacterized genes based on their shared expression patterns with functionally annotated genes. We show that gene expression in common porcine tissues is similar to the expression in homologous tissues of human.Conclusions/SignificanceThe results from this study constitute a valuable and publicly available resource of basic gene expression profiles in normal porcine tissues and will contribute to the identification and functional annotation of porcine genes.
Highlights
The microarray technology is ideal for whole-genome and largescale profiling of gene expression under various conditions
The ratio between the mRNA levels in each tissue and the common reference was computed for all microarray cDNA spots generating 46 sets of relative gene expression profiles for 26.877 porcine cDNAs (PCs)
We further investigated the cDNA sequences and gene expression patterns of this cluster to infer the possible function of the corresponding uncharacterized genes
Summary
The microarray technology is ideal for whole-genome and largescale profiling of gene expression under various conditions. Microarray-based experiments have been widely used to identify differentially expressed genes involved in specific biological processes such as disease or response to environmental stimuli. These experiments have found new gene functions and provide insights into the transcriptional regulation that underlies biological processes. Two-way hierarchical clustering identified expected tissue clusters in accordance with tissue type and a number of cDNA clusters having similar gene expression patterns across tissues For one of these cDNA clusters, we demonstrate that possible tissue associated gene function can be inferred for previously uncharacterized genes based on their shared expression patterns with functionally annotated genes. The results from this study constitute a valuable and publicly available resource of basic gene expression profiles in normal porcine tissues and will contribute to the identification and functional annotation of porcine genes
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