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 shRNA dependency of multiple genes, with the LUNG_SCLC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are ZNF500, DDX58, and ZYG11A, each associated with the pathway in up to 5 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, ZNF500 grouped by Antigen processing and presentation of endogenous antigen-low versus -high activity in LUNG_SCLC.

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
LUNG_SCLC	ZNF500 →	-0.351	-0.259	<.001	<.001	3	5
BLOOD_Lymphoma	DDX58 →	+0.368	+0.370	.003	<.001	3	5
BREAST	ZYG11A →	-0.225	-0.260	.001	.002	3	5
LARGE_INTESTINE	RPS18 →	-0.272	-0.185	.003	.006	3	5
BONE	CCAR2 →	-0.234	-0.375	.003	.001	3	5
PANCREAS	PSMB5 →	-0.555	-0.158	.003	.005	3	5

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

ZNF500 by Antigen processing and presentation of endogenous antigen activity — LUNG_SCLC

Explore this box plot interactively →