Antigen processing and presentation of exogenous peptide antigen

Across TCGA patient cohorts, RNA activity of the Antigen processing and presentation of exogenous 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 PTPN22, CXCL9, and HLA-DQA1, each associated with the pathway in up to 9 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 activity versus PTPN22 in LSCC (Pearson r = 0.56).

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	PTPN22 →	+0.629	+0.281	<.001	<.001	3	9
BRCA	CXCL9 →	+1.615	+0.251	.001	<.001	3	9
GBM	HLA-DQA1 →	+1.185	+0.254	<.001	<.001	3	9
BRCA	IL12RB1 →	+0.755	+0.329	<.001	<.001	3	9
HNSC	TNFSF13B →	+0.807	+0.178	<.001	<.001	3	8
BRCA	CD2 →	+1.060	+0.240	.002	<.001	3	8

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

GO:0002478 vs PTPN22 — LSCC

Explore this scatter interactively →