Figure 4: Networks of experimentally supported direct molecular interactions between genes differentially regulated in neonatal sepsis.
From: Identification of a human neonatal immune-metabolic network associated with bacterial infection
(a) Network relationships derived from InnateDB were visualized with Cytoscape. (Left) Network of direct molecular interactions between genes upregulated in neonatal sepsis patients (shown in red), their encoded products and all other interacting molecules. Inclusion of non-differentially expressed interacting partners (shown in grey) in this network allows potential identification of important regulatory nodes (genes/proteins) not evident from microarray data alone (for example, constitutively expressed nodes/nodes expressed at a time point not sampled in the study). (Middle) The top five hub nodes identified by Degree algorithm of cytoHubba plugin are labelled. Node sizes are defined by the node degree— the larger the node size the higher the degree. Nodes encoded by upregulated genes are shown in red, the top 20 hubs identified by this analysis were STAT1, STAT3, NFKBIA, TNFRF1, CEBPB, SPI1, LYN, BCL6, PRKCD, HCK, MYD88, HSPA1B, UBA1, CEBPD, JUNB, IRF7, TNFAIP3, CTNNA1, ETS2 and GNAI2. (Right) The top-scoring upregulated sub-network identified by jActiveModules plugin. Nodes representing upregulated RNA signals are shown in red; non-differentially expressed genes in grey. (b) Network of molecular interactions directly between genes upregulated in neonatal sepsis patients visualized with the Cerebral v.2 plugin. Nodes encoded by upregulated genes are shown in red; non-differentially expressed interactions partners are not shown. (c) Network of molecular interactions directly between genes downregulated in neonatal sepsis patients visualized with the Cerebral v.2 plugin. Nodes encoded by downregulated genes are shown in green; non-differentially expressed interaction partners are not shown.
