Response to vitamin A

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

The most reproducible pathway-associated genes across cancer lineages are CD6, IL1R1, and PGAM1, each associated with the pathway in up to 3 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, CD6 grouped by Response to vitamin A-low versus -high activity in LUNG_NSCLC_LUAD.

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
LUNG_NSCLC_LUAD	CD6 →	-0.129	-0.750	.004	.003	3	3
CNS	IL1R1 →	-0.341	-0.311	.005	.002	3	3
BLOOD_Leukemia	PGAM1 →	-0.182	-0.236	.005	.009	3	3
CNS	RNF182 →	-0.318	-0.290	.006	.002	3	3
BLOOD_Leukemia	KPNA6 →	-0.147	-0.248	.001	.005	3	3
LARGE_INTESTINE	BRD4 →	+0.397	+0.480	.009	.002	3	3

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

CD6 by Response to vitamin A activity — LUNG_NSCLC_LUAD

Explore this box plot interactively →