GEO dataset analysis

The gene expression profiles of {"type":"entrez-geo","attrs":{"text":"GSE58654","term_id":"58654"}}GSE58654 (3 PBS treated mice, 3 mice with hyperoxia lung injury), {"type":"entrez-geo","attrs":{"text":"GSE130936","term_id":"130936"}}GSE130936 (3 saline treated mice, 3 LPS treated mice), {"type":"entrez-geo","attrs":{"text":"GSE80011","term_id":"80011"}}GSE80011 (3 healthy mice, 3 influenza-virus infected mice), {"type":"entrez-geo","attrs":{"text":"GSE94522","term_id":"94522"}}GSE94522 (3 healthy mice, 3 bleomycin treated mice), {"type":"entrez-geo","attrs":{"text":"GSE21802","term_id":"21802"}}GSE21802 (4 healthy samples; 6 influenza A-induced pneumonia samples without mechanical ventilation), {"type":"entrez-geo","attrs":{"text":"GSE20346","term_id":"20346"}}GSE20346 (18 healthy samples; 6 bacterial pneumonia samples; 4 influenza A-induced pneumonia samples); {"type":"entrez-geo","attrs":{"text":"GSE40012","term_id":"40012"}}GSE40012 (18 healthy samples; 16 bacterial pneumonia samples; 8 influenza A-induced pneumonia samples); {"type":"entrez-geo","attrs":{"text":"GSE76293","term_id":"76293"}}GSE76293 (10 healthy samples; 12 acute respiratory distress syndrome (ARDS) samples) were acquired from the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) database. All of the analysed datasets concern processes associated with acute lung injury in mice at a time point earlier than 24 h after the induction and in humans at day 1 after admission. The characteristics of used datasets are presented in S1 Table.

The identification of differentially expressed genes (DEGs) between healthy mice and mice with ALI was performed using GEO2R, a web service that allows the comparison of two or more datasets in GEO series for DEGs identification across experimental conditions [48]. The adjusted p-values were applied to correct the false positive results by the default Benjamin-Hochberg false discovery rate method. The adjusted p < 0.05 and |Fold Change| > 1.5 were viewed as the cutoff values. A Venn diagram analysis of revealed DEGs was performed using Venny v. 2.0 tool (https://bioinfogp.cnb.cs/tools/venny/).