Response to vitamin A

Across TCGA cell cohorts, RNA activity of the Response to vitamin A pathway is significantly associated with the RNA expression of multiple genes, with the URINARY_TRACT cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are AFF1, KRT2, and AKR7L, each associated with the pathway in up to 4 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, AFF1 grouped by Response to vitamin A-low versus -high activity in URINARY_TRACT.

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
URINARY_TRACT	AFF1 →	-0.839	-1.728	.002	<.001	3	4
PANCREAS	KRT2 →	+0.050	+0.849	.001	.001	3	4
SOFT_TISSUE	AKR7L →	-0.327	-1.011	.004	.004	3	3
BLOOD_Myeloma	MGA →	+0.971	+1.278	.004	<.001	3	3
LUNG_NSCLC_LUSC	PICK1 →	-1.413	-1.477	.005	<.001	3	3
URINARY_TRACT	PDLIM5 →	-1.183	-1.494	<.001	<.001	3	3

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

AFF1 by Response to vitamin A activity — URINARY_TRACT

Explore this box plot interactively →