Functional annotation of the targeted module

Gene enrichment analysis of the categorical biological processes of gene ontology (GO) was conducted on the targeted modules associated with GC patient survival to explore further insights into the genes via the DAVID annotation tool (http://david.abcc.ncifcrf.gov/) (Dennis Jr et al., 2003). The fold enrichment was calculated for all GO terms in the given ontologies to examine the enrichment degree of the specific genes for all genes on the array. Multiple tests were performed with p-values adjusted according to the Bonferroni, Benjamini and false discovery rate (FDR) methods.

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for genes in the targeted module was conducted via the ClueGO (Bindea et al., 2009) and CluePedia (Bindea, Galon & Mlecnik, 2013) applications in the Cytoscape v3.3.0 software. Only terms with p-values <0.05 were retained.