One-carbon metabolic process

Across TCGA cell cohorts, RNA activity of the One-carbon metabolic process 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 RPS7, MAT2A, and LY6G6F, 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, RPS7 grouped by One-carbon metabolic process-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	RPS7 →	+0.199	+0.894	.002	.002	3	4
LUNG_NSCLC_LUAD	MAT2A →	-0.364	-0.408	.001	.003	3	4
LUNG_NSCLC_LUAD	LY6G6F →	-0.188	-0.343	<.001	<.001	3	4
LARGE_INTESTINE	TYMS →	-0.457	-0.723	.004	.007	3	4
SOFT_TISSUE	AP3M2 →	+0.114	+0.893	.008	.002	3	3
KIDNEY	SHMT2 →	-0.293	-1.027	.001	.001	2	4

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

RPS7 by One-carbon metabolic process activity — KIDNEY

Explore this box plot interactively →