Antigen processing and presentation of endogenous peptide antigen

Across TCGA pan-cancer cohorts, RNA activity of the Antigen processing and presentation of endogenous peptide antigen pathway is associated with patient survival in 23 of 34 cancer lineages. Pathway activity is summarized from the expression of its 25 member genes.

The strongest signal is observed in skin cutaneous melanoma (SKCM), where higher Antigen processing and presentation of endogenous peptide antigen 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 BRCA, show the opposite pattern, with higher activity associated with better survival.

SKCM, BRCA, and LGG 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	0.841	0.723	<.001	120	view →
BRCA	OS	Median	All	0.625	0.500	<.001	100	view →
LGG	DFS	Quartile	All	0.224	0.469	<.001	40	view →
MESO	DFS	Tertile	II,III,IV	0.531	0.268	.007	34	view →
UVM	DFS	Median	All	0.330	0.591	.006	34	view →
ACC	OS	Median	All	0.929	0.455	.005	30	view →
CESC	OS	Tertile	IV	0.622	0.195	.018	28	view →
KIRC	DFS	Median	All	0.549	0.687	.001	23	view →
LIHC	OS	Median	III,IV	0.874	0.570	.003	17	view →
BLCA	OS	Tertile	III,IV	0.598	0.306	.013	16	view →
SCLC	DFS	Tertile	All	0.785	0.426	<.001	14	view →
KIRP	OS	Tertile	III,IV	0.443	0.719	.032	13	view →

Pink = unfavorable, green = favorable. Showing the 12 strongest of 23 lineages.

GO:0002483–SKCM (OS)

Open the SKCM breakdown →