Pigment granule organization

Across TCGA cell cohorts, RNA activity of the Pigment granule organization pathway is significantly associated with the shRNA dependency of multiple genes, with the STOMACH cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are CFAP52, ANK3, and KCNJ16, each associated with the pathway in up to 4 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, CFAP52 grouped by Pigment granule organization-low versus -high activity in STOMACH.

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
STOMACH	CFAP52 →	-0.180	-0.296	.006	.002	3	4
LARGE_INTESTINE	ANK3 →	+0.112	+0.161	.001	<.001	3	3
SKIN	KCNJ16 →	-0.196	-0.276	.002	<.001	3	3
UPPER_AERODIGESTIVE_TRACT	ECM2 →	-0.090	-0.182	.009	.005	3	3
UPPER_AERODIGESTIVE_TRACT	PLXDC2 →	-0.172	-0.182	.001	.005	3	3
SKIN	CRISP3 →	+0.188	+0.251	.002	.006	2	4

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

CFAP52 by Pigment granule organization activity — STOMACH

Explore this box plot interactively →