Antigen processing and presentation

Across TCGA pan-cancer cohorts, RNA activity of the Antigen processing and presentation pathway is associated with patient survival in 21 of 34 cancer lineages. Pathway activity is summarized from the expression of its 116 member genes.

The strongest signal is observed in skin cutaneous melanoma (SKCM), where higher Antigen processing and presentation pathway activity is associated with better overall survival. In most high-consensus cancer types, elevated pathway activity shows an unfavorable survival association, although some cancer types, such as SKCM and HNSC, show the opposite pattern, with higher activity associated with better survival.

SKCM, HNSC, and UVM are the cancer lineages in which this pathway most reproducibly stratifies patient survival.

Pathway-activity survival associations by lineage

Ranked by sampling consensus. AUC1 and AUC2 represent the survival AUCs for the high- and low-pathway-activity groups, respectively. The group with the lower AUC is interpreted as having poorer survival. The reported p-values are derived from the log-rank test.

Lineage	Measure	Split	Stage	AUC1 high	AUC2 low	p	Sampling consensus
SKCM	OS	Median	All	0.425	0.254	<.001	132	view →
HNSC	DFS	Tertile	II,III,IV	0.736	0.591	<.001	130	view →
UVM	OS	Tertile	All	0.359	0.710	<.001	65	view →
BRCA	DFS	Median	All	0.580	0.469	.002	53	view →
LUAD	DFS	Median	All	0.742	0.602	<.001	48	view →
LGG	DFS	Median	All	0.316	0.485	<.001	48	view →
LIHC	DFS	Quartile	II,III,IV	0.607	0.322	.002	46	view →
CESC	OS	Quartile	All	0.865	0.700	.012	36	view →
LAML	DFS	Median	All	0.249	0.503	.005	30	view →
ACC	DFS	Median	All	0.744	0.486	.013	30	view →
KIRP	OS	Tertile	III,IV	0.238	0.809	.003	24	view →
MESO	OS	Median	All	0.657	0.438	.002	23	view →

Pink = unfavorable, green = favorable. Showing the 12 strongest of 21 lineages.

GO:0019882–SKCM (OS)

Open the SKCM breakdown →