Fig. 1

Details of PorSignDB. a Overview of the pipeline. 88 curated studies with data from 1776 microarrays chips were retrieved from the GEO repository. Data from each study was uniformly normalized using Genepattern, and gene expression signatures representing each phenotype of every pairwise comparison were calculated in R. Systematical annotations were added to every signature, yielding 412 gene sets. PorSignDB logo was made by NVR. b Example of signature generation. GSE7313 is a study mapping transcript abundance in mesenteric lymph nodes of pigs infected with Salmonella Typhimurium at different time points. The first pair compares data from lymph nodes of uninfected pigs (Phenotype1) with those of pigs 8 h post S. Typhimurium infection (Phenotype2). Significantly upregulated and downregulated genes were selected with a mutual-information based metric, respectively recapitulating highly expressed genes in the ‘uninfected’ phenotype (UP gene set), and highly expressed genes in the ‘8 h post S. Typhimurium infection’ phenotype (DN gene set). Clip art was made by NVR. c Samples were derived from a variety of different tissues, d covering studies in a wide range of different biological themes. e Performance of PorSignDB LPS gene signatures in alveolar macrophages of lungs treated with either LPS or saline solution. f Performance of PorSignDB myocardial infarction gene signatures in myocardial tissue of wild type VS IRF3^−/− knockout mice