Regulation of antigen processing and presentation of peptide antigen

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

The most reproducible pathway-associated genes across cancer lineages are POLR2D, CCR5, and HLA-DQA1, 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 scatter plot shows the strongest association, Regulation of antigen processing and presentation of peptide antigen activity versus POLR2D in LSCC (Pearson r = -0.32).

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
LSCC	POLR2D →	-0.511	-0.576	<.001	.003	3	4
LSCC	CCR5 →	+0.882	+0.727	<.001	<.001	3	4
GBM	HLA-DQA1 →	+1.417	+0.146	<.001	<.001	3	4
GBM	HLA-DOA →	+1.324	+0.190	<.001	<.001	3	4
GBM	MICB →	+0.637	+0.140	.001	<.001	3	4
LSCC	HLA-F →	+0.722	+0.443	<.001	.007	3	4

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

GO:0002583 vs POLR2D — LSCC

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