Antigen processing and presentation of endogenous antigen

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

The most reproducible pathway-associated genes across cancer lineages are VAMP7, BIN1, and PCLAF, each associated with the pathway in up to 4 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 box plot shows the strongest association, VAMP7 grouped by Antigen processing and presentation of endogenous antigen-low versus -high activity in OVARY.

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
OVARY	VAMP7 →	+0.798	+0.827	.009	.006	3	4
SOFT_TISSUE	BIN1 →	+2.100	+1.116	.005	.001	3	3
SOFT_TISSUE	PCLAF →	+1.191	+1.493	.004	<.001	3	3
SOFT_TISSUE	CYP27C1 →	+1.400	+1.305	<.001	<.001	3	3
SKIN	A4GNT →	+0.119	+0.566	<.001	.001	3	3
LUNG_NSCLC_LUSC	MINPP1 →	+0.781	+1.377	<.001	.002	3	3

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

VAMP7 by Antigen processing and presentation of endogenous antigen activity — OVARY

Explore this box plot interactively →