Table 1: Pathway Analysis of Patient-Matched Melanoma Brain and Extracranial Metastases.

Results of EGSEA analyses of 35 MBMs and 42 patient-matched ECMs (from 29 patients). “Gene Set” lists the database (MSigDB, GeneSetDB, or 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-value<0.001.

Gene Set	Summary
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

EGSEA, sort by median rank (adj.p.val <0.001)