Regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II

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

The most reproducible pathway-associated genes across cancer lineages are SCAT1, CCL2, and CTSL, each associated with the pathway in up to 5 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 or polysaccharide antigen via MHC class II activity versus SCAT1 in HNSC (Pearson r = 0.31).

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
HNSC	SCAT1 →	+0.611	+0.584	<.001	.005	2	5
GBM	CCL2 →	+1.522	+0.109	<.001	<.001	3	4
GBM	CTSL →	+0.839	+0.088	<.001	<.001	3	4
GBM	DDX25 →	-0.869	-0.085	<.001	.001	3	3
OV	OASL →	+0.944	+0.111	.006	<.001	3	3
GBM	NCEH1 →	+0.693	+0.098	<.001	<.001	3	3

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

GO:0002580 vs SCAT1 — HNSC

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