Negative regulation of secondary metabolite biosynthetic process

Across TCGA patient cohorts, RNA activity of the Negative regulation of secondary metabolite biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the GBM cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PNKP, HMGN1P13, and WDFY3-AS2, 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 scatter plot shows the strongest association, Negative regulation of secondary metabolite biosynthetic process activity versus PNKP in GBM (Pearson r = -0.21).

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
GBM	PNKP →	-0.372	-0.477	<.001	.009	3	3
LUAD	HMGN1P13 →	+0.539	+0.876	<.001	<.001	3	3
CCRCC	WDFY3-AS2 →	+0.350	+0.603	.005	.001	3	3
CCRCC	SCARNA21B →	-0.497	-0.583	<.001	.002	3	3
UCEC	MAP1B →	+0.897	+0.299	<.001	.002	3	2
HNSC	F3 →	-1.497	-0.151	.002	.002	3	2

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

GO:1900377 vs PNKP — GBM

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