R-based bioinformatics analysis identifies Irf1 as a key up-regulated gene in LPS-exposed murine lung endothelial cells
R-based bioinformatics analysis of published microarray data (GEO acc no. GSE5883) in which cultured human lung microvascular endothelial cells (HLMVECs) were left untreated (Ctrl) or exposed to LPS (10 ng) for 4 h (n = 4 biological replicates per group). (A) Gene set enrichment analysis (GSEA)-based identification of two discreet gene co-expression modules associated with LPS exposure: M1 and M2. Red coloring denotes a positive NES score, while blue coloring denotes a negative NES score. (B) Network plots for the two gene co-expression modules M1 and M2. (C) Reactome enrichment analysis for the two gene co-expression modules M1 and M2. The color saturation denotes the prediction confidence. (D) Volcano plots of differentially expressed genes (DEGs) with staining for M1 module membership (blue, top panel) or M2 module membership (pink, bottom panel). (E) Heatmap of the top 50 M2 module up-regulated DEGs ordered by descending log2 fold-change. Up-regulation is denoted by green coloring, while down-regulation is denoted by red coloring. IRF1 is marked by a red rectangle.