RNA methylation

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

The most reproducible pathway-associated genes across cancer lineages are RAC1, ZNF524, and GAL3ST3, each associated with the pathway in up to 6 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, RAC1 grouped by RNA methylation-low versus -high activity in LARGE_INTESTINE.

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
LARGE_INTESTINE	RAC1 →	-0.522	-0.047	.006	.003	2	6
SKIN	ZNF524 →	-0.217	-0.036	.003	.002	3	4
KIDNEY	GAL3ST3 →	+0.275	+0.073	.004	.006	3	4
LARGE_INTESTINE	SLC19A1 →	+0.125	+0.035	<.001	.001	3	4
UPPER_AERODIGESTIVE_TRACT	METTL2B →	+0.305	+0.047	<.001	.003	3	4
KIDNEY	DOP1B →	+0.428	+0.058	.001	.006	3	4

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

RAC1 by RNA methylation activity — LARGE_INTESTINE

Explore this box plot interactively →