Negative regulation of antigen processing and presentation

Across TCGA patient cohorts, RNA activity of the Negative regulation of antigen processing and presentation 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 CSE1L, HLA-DMA, and SLFN14, 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, Negative regulation of antigen processing and presentation activity versus CSE1L in LSCC (Pearson r = -0.37).

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	CSE1L →	-0.638	-0.223	<.001	<.001	3	5
LUAD	HLA-DMA →	+0.842	+0.288	<.001	.003	3	5
LUAD	SLFN14 →	+0.330	+0.356	<.001	<.001	3	5
LSCC	TTK →	-0.855	-0.181	.003	.002	3	5
LSCC	NUF2 →	-0.893	-0.166	<.001	.001	3	5
LSCC	CDK1 →	-0.894	-0.239	<.001	<.001	3	5

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

GO:0002578 vs CSE1L — LSCC

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