L-serine biosynthetic process

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

The most reproducible pathway-associated genes across cancer lineages are PHGDH, IGFBP6, and PSPH, 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 scatter plot shows the strongest association, L-serine biosynthetic process activity versus PHGDH in CNS (Pearson r = 0.61).

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
CNS	PHGDH →	+1.509	+0.547	.001	.003	3	6
LIVER	IGFBP6 →	-3.872	-0.672	<.001	<.001	3	6
BREAST	PSPH →	+1.552	+0.377	<.001	<.001	3	6
BONE	SYTL3 →	-1.877	-0.447	<.001	.001	3	6
BONE	ACTN4 →	-1.505	-0.399	.002	.007	3	5
BLOOD_Myeloma	CASKIN1 →	+0.306	+0.354	.007	.009	2	6

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

GO:0006564 vs PHGDH — CNS

Explore this scatter interactively →