2.4 Functional enrichment analysis
Gene ontology (GO) is a tool used for gene annotation that functions
through the utilization of a defined, structured, and controlled
vocabulary, including 3 categories,
namely biological processes (BP),
cellular components (CC), and molecular functions (MF) (Ashburner et
al., 2000). The Kyoto Encyclopedia of Genes and Genomes (KEGG) is a
database used to assign sets of DEGs to specific pathways (Kanehisa and
Goto, 2000). The Database for Annotation, Visualization, and Integrated
Discovery (DAVID)
(https://david.ncifcrf.gov/)
is an online database that offers gene enrichment analysis and
functional annotation clustering from various genomic resources (Huang
et al., 2009). GO and KEGG pathway analysis on significant DEGs was
conducted using the DAVID database. The species selected was Homo
sapiens , and the ”adjusted P value < 0.05” was considered to
be of statistical significance.
2. 5
Analysis of protein‐protein interaction (PPI) networks
The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING)
(https://string-db.org/cgi/input.pl)
is an online database, which can predict interactions of proteins by
neighborhood, gene fusion, co-occurrence, co-expression experiments,
databases, and text-mining (Szklarczyk et al., 2015). Significant DEGs
were mapped into PPIs and a combined score of >0.4 was set
as a threshold value in this study. More specifically, nodes with higher
degrees of interaction were considered as hub nodes.