Table 2. Enriched pathways in tumour samples with high CD8⁺ TIL identified by gene set enrichment analysis using pathway definitions from BIOCARTA and KEGG.

Pathway	Database	P-value	FDR	Enriched in
Ribosome pathway	KEGG	0.0	0.0	Low CD8+ TIL
Antigen processing and presentationa	KEGG	0.0	0.0	High CD8+ TIL
Type I diabetes mellitus	KEGG	0.0	0.006	High CD8+ TIL
Toll like receptor signalling pathway	KEGG	0.0	0.055	High CD8+ TIL
Haematopoietic cell lineagea	KEGG	0.0	0.060	High CD8+ TIL
Cytokine cytokine receptor interactiona	KEGG	0.0	0.104	High CD8+ TIL
Cell adhesion moleculesa	KEGG	0.0	0.137	High CD8+ TIL
Citrate cycle	KEGG	0.013	0.156	High CD8+ TIL
Reductive carboxylate cycle	KEGG	0.038	0.142	High CD8+ TIL
CTL pathwaya	BIOCARTA	0.0	0.051	High CD8+ TIL
COMP pathway	BIOCARTA	0.0	0.008	High CD8+ TIL
MITOCHONDRIA pathway	BIOCARTA	0.0	0.120	High CD8+ TIL
D4GDI pathway	BIOCARTA	0.005	0.105	High CD8+ TIL
AMI pathway	BIOCARTA	0.005	0.225	High CD8+ TIL
DC pathwaya	BIOCARTA	0.007	0.215	High CD8+ TIL
TALL1 pathwaya	BIOCARTA	0.010	0.201	High CD8+ TIL
ATRBRCA pathway	BIOCARTA	0.017	0.205	High CD8+ TIL
CSK pathway	BIOCARTA	0.024	0.195	High CD8+ TIL
CASPASE pathway	BIOCARTA	0.029	0.183	High CD8+ TIL
STEM pathway	BIOCARTA	0.037	0.230	High CD8+ TIL
T CYTOTOXIC PATHWAYa	BIOCARTA	0.038	0.198	High CD8+ TIL
ATM pathway	BIOCARTA	0.038	0.198	High CD8+ TIL
LAIR pathway	BIOCARTA	0.046	0.231	High CD8+ TIL

Abbreviations: TIL=tumour-infiltrating lymphocyte; FDR=false discovery rate; KEGG=Kyoto Encyclopedia of Genes and Genomes.

^aAlso associated with improved survival in 157 previously profiled advanced-stage ovarian cancer patients (Crijns et al, 2009).