Antigen processing and presentation of endogenous peptide antigen

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

The most reproducible pathway-associated genes across cancer lineages are PSMB5, DDX58, and EP300, each associated with the pathway in up to 6 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, PSMB5 grouped by Antigen processing and presentation of endogenous peptide antigen-low versus -high activity in BLOOD_Leukemia.

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
BLOOD_Leukemia	PSMB5 →	-0.640	-0.253	.002	.003	2	6
BLOOD_Lymphoma	DDX58 →	+0.368	+0.353	.003	<.001	3	5
LUNG_NSCLC_LUAD	EP300 →	-0.253	-0.132	.002	.007	3	5
LUNG_NSCLC_LUSC	PSMB6 →	-0.603	-0.318	.001	<.001	3	4
LARGE_INTESTINE	GTF2IRD1 →	-0.267	-0.246	<.001	<.001	3	4
LUNG_NSCLC_LUSC	OR2K2 →	+0.221	+0.241	.008	.008	2	5

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

PSMB5 by Antigen processing and presentation of endogenous peptide antigen activity — BLOOD_Leukemia

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