Antigen processing and presentation of peptide antigen

Across TCGA cell cohorts, RNA activity of the Antigen processing and presentation of peptide antigen pathway is significantly associated with the RNA expression of multiple genes, with the LIVER cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PSMB9, B2M, and HLA-C, each associated with the pathway in up to 16 cancer types. Since the analysis shows associations rather than directional relationships, both pathway-to-partner and partner-to-pathway views are reported.

Each partner is linked to its corresponding Q-omics profile. The scatter plot shows the strongest association, Antigen processing and presentation of peptide antigen activity versus PSMB9 in LIVER (Pearson r = 0.71).

Pathway-associated genes by consensus

Ranked by combined sampling and lineage consensus. X-score (pathway→partner) and Y-score (partner→pathway) are standardized regression coefficients; both directions are reported because the association is undirected. The reported p-values are derived from the association test.

Lineage	Partner gene	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
LIVER	PSMB9 →	+4.935	+0.458	.006	<.001	3	16
LARGE_INTESTINE	B2M →	+2.474	+0.408	.001	.002	3	15
CNS	HLA-C →	+3.493	+0.433	.002	.003	3	15
LIVER	PSMB8 →	+4.444	+0.436	.003	.007	3	14
LIVER	TAP1 →	+3.650	+0.443	.004	.005	3	13
SOFT_TISSUE	HLA-A →	+3.018	+0.292	.007	.001	2	14

Each partner links to its Q-omics profile. Showing the 6 strongest associations by consensus.

GO:0048002 vs PSMB9 — LIVER

Explore this scatter interactively →