Glycine biosynthetic process

Across TCGA cell cohorts, RNA activity of the Glycine biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the URINARY_TRACT cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SHMT1, ATPAF2, and MED9, each associated with the pathway in up to 20 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 scatter plot shows the strongest association, Glycine biosynthetic process activity versus SHMT1 in URINARY_TRACT (Pearson r = 0.85).

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
URINARY_TRACT	SHMT1 →	+1.752	+0.249	<.001	<.001	3	20
OESOPHAGUS	ATPAF2 →	+0.969	+0.167	.008	.001	2	19
BLOOD_Leukemia	MED9 →	+0.802	+0.144	<.001	<.001	3	14
BLOOD_Lymphoma	COPS3 →	+0.902	+0.119	<.001	<.001	3	14
BREAST	ALKBH5 →	+0.844	+0.215	<.001	<.001	3	14
LARGE_INTESTINE	RPA1 →	+0.924	+0.147	<.001	<.001	3	14

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

GO:0006545 vs SHMT1 — URINARY_TRACT

Explore this scatter interactively →