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Published on: January 30, 2017
Assessment of the swine protein-annotated oligonucleotide microarray
J P Steibel1, M Wysocki, J K Lunney
1Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA. steibelj@msu.edu
Animal Genetics
|June 12, 2009
Summary
The swine protein-annotated oligonucleotide microarray (Pigoligoarray) effectively profiles gene expression across four porcine tissues. This tool aids agricultural research and biomedical studies by identifying differentially expressed genes and enabling comparisons with human gene orthologs.
Area of Science:
- Genomics and Bioinformatics
- Animal Science
- Biomedical Research
Background:
- The need for robust tools to analyze gene expression in swine is critical for both agricultural applications and as a biomedical model.
- Existing methods require validation for specificity and utility in complex biological samples.
Purpose of the Study:
- To evaluate the specificity and utility of the swine protein-annotated oligonucleotide microarray (Pigoligoarray).
- To develop tools for comparative analysis of gene expression data, including human ortholog mapping.
- To identify differentially expressed transcripts in key porcine tissues.
Main Methods:
- Profiling transcript expression in liver, brain stem, longissimus dorsi muscle, and uterine endothelium from four pigs using the Pigoligoarray.
- Developing comparative analysis tools, including HGNC identities and human ortholog alignments.
- Utilizing perfect match (PM) and mismatch (MM) probes for assessing hybridization specificity and introducing diagnostic analyses.
Main Results:
- Out of 20,400 oligonucleotides, 12,429 transcripts were found to be putatively differentially expressed.
- Tissue-specific expression analyses identified significant numbers of differentially expressed genes in liver (958), muscle (726), uterine endothelium (286), and brain stem (1027).
- Quantitative PCR (QPCR) confirmed hybridization results, and comparisons with human orthologs validated the array's utility.
Conclusions:
- The Pigoligoarray is a specific and useful tool for profiling gene expression in swine.
- The developed comparative analysis tools enhance data interpretation and cross-species comparisons.
- This microarray platform supports both agricultural advancements and the use of pigs as biomedical models for human diseases.
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