Metacore software

Pathway analysis was performed to explore the characteristics of the genes detected in each analysis or genes to which detected isoforms belong. We used MetaCore software (version 6.24 build 67895, Thomson Reuters, NY, USA) with high-quality, manually curated content and the PANTHER Classification System (PANTHER 17.0) (64 (link)) to validate the results of MetaCore software. The Gene Ontology database (65 (link), 66 (link)) was used to search for significant gene sets. We searched a maximum of the top 500 gene sets in the MetaCore analysis that met the following conditions: (i) FDR < 0.05 in MetaCore and replicated in PANTHER with P < 0.05; (ii) if a pathway contains fewer than 100 network objects, at least 10% of them are included in the test gene set; (iii) if a pathway has more than 100 network objects, at least 10 objects are included in the test gene set; and (iv) the total number of objects in the pathway is less than 3000. When more than 10 pathways were detected, Cytoscape (67 (link)) was used to show the relationships among the top 10 pathways. The coordinates, which indicated the positional relationship between pathways, used the first and second principal components calculated based on the presence or absence of the included network objects.

MetaCore™ software (version 19.3; Thomson Reuters, NY) is a pathway analysis tool based on a proprietary manually curated database of human protein–protein, protein–DNA and protein compound interactions. MetaCore pathway analysis by GeneGo was performed using genes showing epigenomic and genomic alterations in T samples belonging to each cluster. Such genes were considered significantly enriched in pathways for which the false discovery rate (FDR) was less than 0.05.

Metacore software (Thomson Reuters, MI, USA) was used to perform functional enrichment analysis and to create biological protein networks. Enriched pathways were considered significant at p value < 0.05.

MetaCore™ software (version 19.3; Thomson Reuters, New York, NY, USA) is a pathway analysis tool based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions. MetaCore pathway analysis by GeneGo was performed using genes showing significant differences in DNA methylation levels among recurrence risk classification categories. Such genes were considered significantly enriched in pathways for which the p-value was less than 0.01.