Antigen processing and presentation

Across TCGA patient cohorts, RNA activity of the Antigen processing and presentation pathway is significantly associated with the protein abundance of multiple proteins, with the HNSC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are RCSD1, RIN3, and SAMSN1_S23, each associated with the pathway in up to 10 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 activity versus RCSD1 in HNSC (Pearson r = 0.29).

Pathway-associated proteins 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 protein	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
HNSC	RCSD1 →	+0.637	+0.067	<.001	<.001	3	10
GBM	RIN3 →	+0.457	+0.094	<.001	<.001	3	10
BRCA	SAMSN1_S23 →	+0.989	+0.046	<.001	<.001	3	10
GBM	SASH3 →	+0.551	+0.115	<.001	<.001	3	10
GBM	SEPTIN1 →	+1.029	+0.110	<.001	<.001	3	10
GBM	SKAP2 →	+0.841	+0.114	<.001	<.001	3	10

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

GO:0019882 vs RCSD1 — HNSC

Explore this scatter interactively →