tRNA pseudouridine synthesis

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

The most reproducible pathway-associated genes across cancer lineages are SGF29, PER1, and CYP2D6, 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, SGF29 grouped by tRNA pseudouridine synthesis-low versus -high activity in SOFT_TISSUE.

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
SOFT_TISSUE	SGF29 →	+0.654	+1.696	<.001	<.001	3	4
LUNG_NSCLC_LUSC	PER1 →	+1.268	+1.564	.004	.004	3	4
BREAST	CYP2D6 →	+0.897	+1.128	<.001	<.001	3	4
KIDNEY	TUFT1 →	-1.496	-1.582	.001	.003	3	4
BLOOD_Lymphoma	PARD6A →	-2.125	-1.755	.009	<.001	3	3
LARGE_INTESTINE	SNAPC2 →	-0.774	-1.175	.002	.004	3	3

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

SGF29 by tRNA pseudouridine synthesis activity — SOFT_TISSUE

Explore this box plot interactively →