Phosphatidylcholine biosynthetic process

Across TCGA cell cohorts, RNA activity of the Phosphatidylcholine biosynthetic process pathway is significantly associated with the shRNA dependency of multiple genes, with the CNS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SCN9A, HCFC2, and SGTA, each associated with the pathway in up to 3 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, SCN9A grouped by Phosphatidylcholine biosynthetic process-low versus -high activity in CNS.

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	SCN9A →	+0.327	+0.821	<.001	.007	3	3
LUNG_NSCLC_LUAD	HCFC2 →	-0.166	-0.845	.008	.007	3	3
SKIN	SGTA →	+0.241	+1.225	.001	.001	3	3
SKIN	TBX20 →	-0.141	-1.062	<.001	.001	3	3
LARGE_INTESTINE	KLF3 →	-0.212	-1.410	<.001	<.001	3	3
LARGE_INTESTINE	FABP4 →	-0.091	-0.687	.009	.008	3	3

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

SCN9A by Phosphatidylcholine biosynthetic process activity — CNS

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