Nucleolus organization

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

The most reproducible pathway-associated genes across cancer lineages are KHK, PHC3, and GSR, 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, KHK grouped by Nucleolus organization-low versus -high activity in KIDNEY.

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
KIDNEY	KHK →	-0.140	-0.058	.001	<.001	3	5
URINARY_TRACT	PHC3 →	+0.322	+0.127	<.001	<.001	3	4
LIVER	GSR →	+0.189	+0.100	.002	.004	3	4
LIVER	CTHRC1 →	+0.271	+0.131	.001	.003	3	4
LARGE_INTESTINE	DDIT4 →	+0.189	+0.065	.005	.002	3	4
KIDNEY	AGTR2 →	+0.234	+0.073	.003	.001	3	4

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

KHK by Nucleolus organization activity — KIDNEY

Explore this box plot interactively →