Fig. 3

Leukocyte genomic responses in patients with community-acquired pneumonia with direct or delayed admission to the intensive care unit. A Volcano plots illustrating the differences in leukocyte genomic responses (integrating log2-fold changes and multiple-test adjusted probabilities) between patients with direct admission to the ICU for community-acquired pneumonia (CAP) and healthy subjects (left), and patients with delayed admission for CAP and healthy subjects (right). Considering adjusted P < .05, 8712 and 7968 genes were identified as differentially expressed in patients admitted directly of with delay for CAP vs healthy subjects, respectively. Blue dots represent significantly underexpressed genes (adjusted P < .05, fold expression < − 1.2), whereas red dots represent significantly overexpressed genes (adjusted P < .05, fold expression > 1.2) in patients relative to healthy controls. Horizontal dotted line indicates multiple-test adjusted Benjamini–Hochberg (BH) P < .05 threshold. Within plots, pie charts show the extent of gene expression changes: blue slices show significantly underexpressed genes (adjusted P < .05 and expression more than 1.2-times decreased compared with healthy controls), red slices show significantly overexpressed genes (adjusted P < .05 and expression more than 1.2-time increased compared with healthy controls), and grey slices show significantly different gene expression (adjusted P < .05 and expression less than 1.2-time increased or decreased compared with healthy controls). B Venn–-Euler representation of differentially expressed genes on admission in CAP patients with direct or delayed ICU-admission vs healthy subjects (adjusted P < .05). Red arrows denote overexpressed genes, blue arrows denote underexpressed genes. C Dot plot depicting the common response (log2-fold changes) of CAP patients with direct or delayed ICU-admission as compared with healthy subjects. Rho, Spearman’s correlation coefficient. D Volcano plot illustrating the differences in leukocyte genomic responses on admission between patients with delayed compared with direct admission to the ICU for community-acquired pneumonia (CAP). Considering adjusted P < .05, 268 genes were differentially expressed. E Considering Benjamini–Hochberg’s adjusted P < .05, underexpressed genes were analysed for association with canonical signalling pathways by Ingenuity pathway analysis (IPA, www.ingenuity.com). Pathways are stratified by significance, which was gauged by BH-adjusted Fisher exact probability. –log (BH) P, negative log transformed BH-adjusted P value. Within plots, pie charts show the extent of gene expression changes in delayed compared to direct admissions for pneumonia