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.