Antigen processing and presentation of peptide antigen via MHC class Ib

Across TCGA patient cohorts, RNA activity of the Antigen processing and presentation of peptide antigen via MHC class Ib pathway is significantly associated with the protein abundance of multiple proteins, with the CCRCC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are TAPBP, IFIT3, and GBP1, 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 peptide antigen via MHC class Ib activity versus TAPBP in CCRCC (Pearson r = 0.35).

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
CCRCC	TAPBP →	+0.689	+0.086	<.001	<.001	3	10
HNSC	IFIT3 →	+1.068	+0.059	<.001	<.001	3	10
CCRCC	GBP1 →	+0.714	+0.079	<.001	<.001	3	10
HNSC	STAT1 →	+0.628	+0.072	<.001	<.001	3	9
PDAC	TAP2 →	+0.867	+0.069	<.001	<.001	3	9
BRCA	DDX60 →	+0.654	+0.056	<.001	<.001	3	9

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

GO:0002428 vs TAPBP — CCRCC

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