ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

The quantity and breadth of genome-scale data sets that examine RNA expression in diverse bacterial and eukaryotic species are increasing more rapidly than for curated knowledge. Our ADAGE method integrates such data without requiring gene function, gene pathway, or experiment labeling, making practical its application to any large gene expression compendium. We built a Pseudomonas aeruginosa ADAGE model from a diverse set of publicly available experiments without any prespecified biological knowledge, and this model was accurate and predictive. We provide ADAGE results for the complete P. aeruginosa GeneChip compendium for use by researchers studying P. aeruginosa and source code that facilitates ADAGE’s application to other species and data types.