Response to retinoic acid

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

The most reproducible pathway-associated genes across cancer lineages are SYT2, NRIP1, and SPTLC2, 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, Response to retinoic acid activity versus SYT2 in LUNG_NSCLC_LUSC (Pearson r = -0.83).

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_LUSC	SYT2 →	-0.090	-0.524	.009	.002	3	5
BLOOD_Myeloma	NRIP1 →	+1.789	+0.224	.004	<.001	3	5
KIDNEY	SPTLC2 →	+1.218	+0.192	.004	.003	3	4
LUNG_NSCLC_LUAD	SIPA1L2 →	-1.298	-0.183	.002	.001	3	4
UPPER_AERODIGESTIVE_TRACT	AP1S1 →	-0.963	-0.216	<.001	.002	3	4
LARGE_INTESTINE	GNPNAT1 →	-0.730	-0.237	.003	.002	3	4

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

GO:0032526 vs SYT2 — LUNG_NSCLC_LUSC

Explore this scatter interactively →