Regulation of phospholipid biosynthetic process

Across TCGA patient cohorts, RNA activity of the Regulation of phospholipid biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the BRCA cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are RAPGEF3, SEPTIN3, and LMNB1, 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, Regulation of phospholipid biosynthetic process activity versus RAPGEF3 in BRCA (Pearson r = 0.03).

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
BRCA	RAPGEF3 →	+0.553	+0.147	.002	<.001	3	6
BRCA	SEPTIN3 →	-1.043	-0.144	<.001	<.001	3	4
BRCA	LMNB1 →	-0.698	-0.124	<.001	<.001	3	4
BRCA	CENPO →	-0.364	-0.091	.001	.004	3	4
BRCA	PTRH2 →	-0.635	-0.170	<.001	<.001	3	4
BRCA	CCT3 →	-0.374	-0.148	<.001	<.001	3	4

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

GO:0071071 vs RAPGEF3 — BRCA

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