Regulation of phosphatidylcholine metabolic process

Across TCGA patient cohorts, RNA activity of the Regulation of phosphatidylcholine metabolic 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 PNP, EFHC1, and AGFG2, each associated with the pathway in up to 5 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 phosphatidylcholine metabolic process activity versus PNP in BRCA (Pearson r = 0.26).

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	PNP →	+0.517	+0.099	.002	.001	3	5
UCEC	EFHC1 →	-0.590	-0.152	.004	.001	3	5
LUAD	AGFG2 →	-0.404	-0.085	.002	<.001	3	4
LSCC	S100A12 →	+1.226	+0.136	<.001	.003	3	4
BRCA	CEP290 →	-0.469	-0.084	<.001	<.001	3	4
UCEC	TRAF5 →	-0.690	-0.150	.007	.003	3	4

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

GO:0150172 vs PNP — BRCA

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