Table 1.

Pathway analysis of patient-matched MBMs and Extracranial Metastases

Gene setSummary
MSigDB: Hallmark signatures
  • Allograft rejection → depleted in MBMs

  • Interferon gamma response → depleted in MBMs

  • IL6–JAK–STAT3 signaling → depleted in MBMs

MSigDB: c5 GO gene sets
  • 18/20 top-ranked gene sets → related to immune system and depleted in MBMs

  • 2/20 top-ranked gene sets → related to nervous system and enriched in MBMs

GeneSetDB: Pathway
  • 18/20 top-ranked gene sets → related to immune system and depleted in MBMs

  • 2/20 top-ranked gene sets → related to nervous system and enriched in MBMs

KEGG: Non-Disease Pathway
  • 4/5 top-ranked gene sets → related to immune system and depleted in MBMs

  • 1/5 top-ranked gene sets → related to nervous system and enriched in MBMs

  • NOTE: Results of EGSEA analyses of 35 MBMs and 42 patient-matched extracranial metastases (from 29 patients). “Gene set” lists the database [MSigDB, GeneSetDB, or Kyoto Encyclopedia of Genes and Genomes (KEGG)] and the specific collection of gene sets (Hallmark and c5: Gene Ontology from MSigDB, Pathway from GeneSetDB, and Non-Disease Pathway from KEGG) included in each analysis. Only nervous system and immune system pathways from these databases are included. Median rank was used to order the top-20 gene sets in each analysis. All gene sets listed have an adjusted P < 0.001. EGSEA, sort by median rank (adj. P < 0.001).