Fig. 7

CEMiTool applied to study Dengue infection. a Expression data from two microarray studies of patients infected or not with Dengue virus were downloaded from GEO. CEMiTool was independently run on those studies using an annotation file, pathway gene set list and protein-protein interaction file. Selected results of the 4 CEMiTool analyses are displayed in panels (b) to (e). b Gene Set Enrichment Analyses showing the module activity on each class of samples. c Profile plots of modules M4 (GSE18090) and M3 (GSE43777). The expression levels of individual genes from each module are shown as colored lines. The black line represents the mean expression of all genes inside the module. Samples are shown in the x-axis and colored by classes. d Over Representation Analysis of modules M4 (GSE18090) and M3 (GSE43777). Bar graphs shows the -log₁₀ Adjusted P-value of the enrichment between genes in modules and gene sets from Reactome Pathway database. The vertical dashed grey line indicates an adjusted P-value of 0.01. e Gene networks of modules M4 (GSE18090) and M3 (GSE43777). The top ten most connected genes (hubs) are labeled and colored based on their “origin”: if originally present in the CEMiTool module, they are colored blue; if inserted from the interactions file, they are colored red. The size of the node is proportional to its degree