Negative regulation of MHC class II biosynthetic process

Across TCGA cell cohorts, RNA activity of the Negative regulation of MHC class II biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the STOMACH cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are VGLL4, CSK, and XPO4, 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 box plot shows the strongest association, VGLL4 grouped by Negative regulation of MHC class II biosynthetic process-low versus -high activity in STOMACH.

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
STOMACH	VGLL4 →	+0.959	+0.859	.002	.004	3	5
BREAST	CSK →	+1.019	+0.876	.001	.005	3	4
BONE	XPO4 →	+0.885	+1.129	.004	.008	3	4
BREAST	NCKIPSD →	+0.681	+0.789	.001	.007	3	4
BLOOD_Myeloma	IGFBP6 →	-2.014	-1.636	.001	.006	3	4
LARGE_INTESTINE	DHDDS →	-0.894	-1.284	.002	.009	3	3

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

VGLL4 by Negative regulation of MHC class II biosynthetic process activity — STOMACH

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