Pigment metabolic process

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

The most reproducible pathway-associated genes across cancer lineages are ALMS1, PKD1, and SLC9A1, 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, Pigment metabolic process activity versus ALMS1 in OESOPHAGUS (Pearson r = -0.63).

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
OESOPHAGUS	ALMS1 →	-0.818	-0.203	.007	.002	3	5
CNS	PKD1 →	+0.811	+0.270	<.001	.001	3	4
LUNG_NSCLC_LUAD	SLC9A1 →	+0.451	+0.138	.007	.005	3	4
LIVER	RASL11A →	+2.290	+0.246	.002	.001	3	4
LUNG_SCLC	TAF1A →	-0.823	-0.191	.001	.001	3	4
CNS	SAMD9L →	+1.474	+0.187	.008	.006	3	4

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

GO:0042440 vs ALMS1 — OESOPHAGUS

Explore this scatter interactively →