Pigment granule localization

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

The most reproducible pathway-associated genes across cancer lineages are SMPD1, POLD4, and TYW1B, 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, SMPD1 grouped by Pigment granule localization-low versus -high activity in LIVER.

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
LIVER	SMPD1 →	-1.703	-1.335	.003	<.001	3	5
BLOOD_Lymphoma	POLD4 →	-2.939	-1.971	<.001	<.001	3	5
SKIN	TYW1B →	-1.036	-1.206	.008	.001	3	5
LIVER	TLN1 →	-1.125	-1.191	<.001	<.001	3	4
LARGE_INTESTINE	ATP6V0D1 →	-0.528	-0.745	.008	.006	3	4
BONE	STK17A →	-1.762	-1.990	.001	<.001	3	4

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

SMPD1 by Pigment granule localization activity — LIVER

Explore this box plot interactively →