Bioinformatics analyses

MetaCore was used to construct biological networks and associated diseases from expressed gene sets in the cDNA microarray. The cutoff level was set to a p value of < 0.05 to determine significant enrichment in the MetaCore database. Gene Set Enrichment Analysis (GSEA) software was applied for enrichment of gene sets that had a common biological function, chromosomal location, or regulation ^23,24. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to perform enrichment analyses for signal pathways ^25-27. We used Fisher's test to select significantly enriched pathways in ampullary cancer. Statistical significance of Gene Ontology (GO) terms was set to a p value of < 0.05. REVIGO software was used to remove any redundancy of GO terms ^28,29. Simulation of Multivariate Linear Model Data (SimRel) for measuring semantic similarity was used with a median of 0.7 for similarity between enriched GO terms. A list of potential genes was mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG), Hallmark, BioCarta, and Reactome for the biological pathway analysis, with a p value of < 0.05 accepted as being statistically significant ^30-32. A flowchart of the analysis is summarized in Supplementary Figure 1.