Antigen processing and presentation of exogenous peptide antigen via MHC class II

Across TCGA patient cohorts, RNA activity of the Antigen processing and presentation of exogenous peptide antigen via MHC class II pathway is significantly associated with the RNA expression of multiple genes, with the LUAD cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PTPN22, HLA-DMA, and HLA-DPA1, 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 of exogenous peptide antigen via MHC class II activity versus PTPN22 in LUAD (Pearson r = 0.38).

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
LUAD	PTPN22 →	+0.843	+0.228	<.001	<.001	3	10
HNSC	HLA-DMA →	+1.055	+0.269	<.001	<.001	3	10
COAD	HLA-DPA1 →	+1.328	+0.175	<.001	<.001	3	10
HNSC	C1QC →	+1.166	+0.191	<.001	<.001	3	10
BRCA	APOBEC3H →	+0.798	+0.254	<.001	<.001	3	9
HNSC	TNFAIP8L2 →	+0.730	+0.223	.001	<.001	3	9

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

GO:0019886 vs PTPN22 — LUAD

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