Abstract
Publicly available genomic data are a great source of biological knowledge that can be extracted when appropriate data analysis is used. Predicting the biological function of genes is of interest to understand molecular mechanisms of virulence and resistance in pathogens and hosts and is important for drug discovery and disease control. This is commonly done by searching for similar gene expression behavior. Here, we used publicly available Streptococcus pyogenes microarray data obtained during primate infection to identify genes that have a potential influence on virulence and Phytophtora infestance inoculated tomato microarray data to identify genes potentially implicated in resistance processes. This approach goes beyond co-expression analysis. We employed a quasi-likelihood model separated by primate gender/inoculation condition to model median gene expression of known virulence/resistance factors. Based on this model, an influence analysis considering time course measurement was performed to detect genes with atypical expression. This procedure allowed for the detection of genes potentially implicated in the infection process. Finally, we discuss the biological meaning of these results, showing that influence analysis is an efficient and useful alternative for functional gene prediction.
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Romeo, J.S., Torres-Avilés, F. & López-Kleine, L. Detection of influent virulence and resistance genes in microarray data through quasi likelihood modeling. Mol Genet Genomics 288, 49–61 (2013). https://doi.org/10.1007/s00438-012-0730-8
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DOI: https://doi.org/10.1007/s00438-012-0730-8