Systems biology analysis
The Ch11q protein-coding genes and miRNA target genes (Supplemental Table S1) identified were used as inputs to generate a Homo sapiens protein-protein interaction (PPI) network by using the STRING database v.11.0 29. To determine interactions of COX-2/PGES1 pathway with Ch11q, PTGS2 was also included in the PPI, together with a list of other 29 inflammation-related genes obtained from two recent reviews 17, 30. All active interaction sources included experiments, databases, co-expression, neighborhood, gene fusion, and co-occurrence, but not textmining. The minimum required interaction score was set at medium confidence (0.400). For topological analyzes, degree, betweenness, and eigenvector centralities were calculated. The PPI data was transferred to the Cytoscape v.3.6.1 software 31, and the CentiScape 2.2 Plug-in was used to select the centralities in the whole network. Degree measures how many direct neighbors are connected to a given node, and nodes with above-average degree values are called hubs. A bottleneck is a node with above-average betweenness, which significantly influences the network structure. Finally, the eigenvector centrality assigns a relative score to all the nodes in the network based on the concept that connections to high-scoring nodes highly contribute to the network31. High eigenvector denotes network switches in the network 32. Nodes with above-average scores in all three centralities are classified as Hub-Bottlenecks-Switches (HBS) and have a key influence in regulating molecular networks.
To better understand the network organization, cluster formation was investigated with the Molecular Complex Detection (MCODE) app33. Loops, Haircut, and Fluff were chosen in the network using the advanced options. The cut-off point was delimited as many nodes > 10 and number of connections > 3. The Biological Networks Gene Ontology tool (BiNGO) plug-in was used to investigate Gene Ontologies 34, with hypergeometric testing and the Bonferroni family-wise correction with a significance level p ≥ 0.05. All non-specific bioprocesses, such as regulation of the biological process, regulation of the metabolic process, were excluded for further analysis considering their lack of biological meaning. The workflow of the used methods is shown in Supplemental Figure S1.