tRNA methylation

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

The most reproducible pathway-associated genes across cancer lineages are PIF1, ARHGEF7, and GAL3ST4, 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, PIF1 grouped by tRNA methylation-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	PIF1 →	+1.481	+1.531	<.001	.001	3	3
LARGE_INTESTINE	ARHGEF7 →	-0.681	-0.188	.001	.006	3	3
LARGE_INTESTINE	GAL3ST4 →	-1.022	-0.244	<.001	.001	3	3
LUNG_NSCLC_LUAD	VPREB1 →	-0.104	-0.561	.005	.002	3	3
LUNG_NSCLC_LUAD	SH2D1A →	-0.057	-0.491	.005	.002	2	4
CNS	ACVR1B →	-0.652	-0.714	.001	.005	3	3

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

PIF1 by tRNA methylation activity — KIDNEY

Explore this box plot interactively →