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 protein abundance of multiple proteins, with the LSCC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are RTN1, WIPF1, 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 RTN1 in LSCC (Pearson r = 0.69).

Pathway-associated proteins 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 protein	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
LSCC	RTN1 →	+0.542	+0.133	<.001	<.001	3	10
UCEC	WIPF1 →	+0.393	+0.136	<.001	.005	3	10
GBM	HLA-DPA1 →	+0.884	+0.133	<.001	<.001	3	10
OV	HLA-DRA →	+0.967	+0.081	<.001	.001	3	10
LSCC	CLIC2 →	+0.634	+0.137	<.001	<.001	3	10
GBM	HLA-DRB5 →	+0.952	+0.122	<.001	<.001	3	10

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

GO:0019886 vs RTN1 — LSCC

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