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 BLOOD_Leukemia cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SPATA7, COG4, and PTPN20, 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, SPATA7 grouped by Pigment metabolic process-low versus -high activity in BLOOD_Leukemia.

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
BLOOD_Leukemia	SPATA7 →	-0.701	-1.115	.001	.005	3	5
BREAST	COG4 →	+0.918	+1.194	<.001	<.001	3	4
SKIN	PTPN20 →	-1.106	-1.003	<.001	<.001	3	4
LARGE_INTESTINE	LAT →	-1.222	-0.906	.003	.003	3	4
LUNG_SCLC	HLA-DMA →	+1.326	+1.563	.008	<.001	3	4
CNS	DENND1A →	+0.467	+0.944	.006	.001	3	3

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

SPATA7 by Pigment metabolic process activity — BLOOD_Leukemia

Explore this box plot interactively →