Pigmentation

Across TCGA cell cohorts, RNA activity of the Pigmentation pathway is significantly associated with the RNA expression of multiple genes, with the LARGE_INTESTINE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are GOLGA4, STBD1, and EHD2, 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, GOLGA4 grouped by Pigmentation-low versus -high activity in LARGE_INTESTINE.

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
LARGE_INTESTINE	GOLGA4 →	-0.800	-1.027	.005	.003	3	4
BONE	STBD1 →	-1.479	-1.172	.009	.006	3	4
OVARY	EHD2 →	-2.695	-1.303	.003	<.001	3	4
BONE	ADAMTSL5 →	-1.964	-1.407	.004	.001	3	4
KIDNEY	TPMT →	-0.496	-0.820	.008	.007	3	4
KIDNEY	SGMS2 →	-0.704	-1.083	.004	.005	2	5

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

GOLGA4 by Pigmentation activity — LARGE_INTESTINE

Explore this box plot interactively →