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Dissecting Inflammatory Complications in Critically Injured Patients by Within-Patient Gene Expression Changes: A Longitudinal Clinical Genomics Study

Figure 5

Dynamic co-expression modules and their dominant trajectories across the five ocMOF subgroups.

We used DAVID to obtain 54 functionally related gene sets from the 3,663 most significant probesets (10% FDR), which were then clustered into five modules according to the similarity of their dominant trajectories across the ocMOF subgroups. Modules A, B, C, D, and E contain 47, 37, 577, 231, and 364 probesets, respectively. We applied IPA to identify enriched pathways within each module. This IPA analysis shortlisted the following pathways as statistically significant (p-value<0.002, after Bonferroni correction; see Table S5): Oxidative Phosphorylation (Module A); RAN, IL-10 and IL-6 signaling, and the Glycosphingolipid Biosynthesis-Lactoseries Pathway (Module C); Allograft Rejection Signaling, Antigen Presentation Pathway, Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells, OX40 Signaling Pathway, Nur77 Signaling in T Lymphocytes (Module D); and Protein Ubiquitination Pathway, Hypoxia Signaling, and Cleavage and Polyadenylation of Pre-mRNA in the Cardiovascular System (Module E). Note that Module A contains 47 probesets and one statistically significant pathway, and Module B contains 37 probesets and no statistically significant pathway.

Figure 5

doi: https://doi.org/10.1371/journal.pmed.1001093.g005