Nucleolar chromatin organization

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

The most reproducible pathway-associated genes across cancer lineages are METTL2A, GPNMB, and GNAI1, 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, METTL2A grouped by Nucleolar chromatin organization-low versus -high activity in SKIN.

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
SKIN	METTL2A →	-0.187	-0.057	<.001	.005	3	5
SKIN	GPNMB →	-0.232	-0.060	.001	.004	3	5
PANCREAS	GNAI1 →	+0.142	+0.100	.002	<.001	3	4
URINARY_TRACT	PDK3 →	+0.286	+0.160	.001	.002	3	4
SKIN	OR4L1 →	+0.183	+0.089	.001	<.001	3	4
LIVER	DPYD →	+0.281	+0.152	.004	.005	3	4

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

METTL2A by Nucleolar chromatin organization activity — SKIN

Explore this box plot interactively →