Statistical Genomics & Bioinformatics

Studying the effects of campylobacter infection in pigs by high throughput gene expression analysis

Campylobacter is the most common source of food poisoning, accounting for over 250,000 cases in the UK and an estimated 9,000,000 in Europe each year. The cost of campylobacteriosis is estimated by the European Food Safety Authority (EFSA) to be €2.4 billion (£1.8 billion) annually. In order to better understand the disease mechanism, BioSS has been working with researchers at the Moredun Research Institute, to identify the genes and biological processes that are altered during infection with Campylobacter from gene expression profiles generated by microarray technology using the pig gastrointestinal system as a model. Samples are prepared from control and infected samples from the colon and ileum and subject to statistical analyses that identify genes whose expression level between conditions are significantly different. Gene set enrichment analysis (GSEA) approaches are then used to find the key biological pathways represented and to prioritise the genes themselves. In addition to confirming host genes and processes already implicated in existing Campylobacter infection studies, many novel high priority genes have been identified and are being validated experimentally.

volcano plot of genes Volcano plot of genes showing at least 2-fold differential expression between control and campylobacter infected colon samples with false discovery rate (fdr) set at 5% (blue). Genes that fail to pass the fdr and fold-change thresholds (red).

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Ian Nevison

Article date 2015

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