Positive regulation of secondary metabolite biosynthetic process

Across TCGA cell cohorts, RNA activity of the Positive regulation of secondary metabolite 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 RFC5, MYG1, and GEMIN2, 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 box plot shows the strongest association, RFC5 grouped by Positive regulation of secondary metabolite 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	RFC5 →	+0.640	+0.797	<.001	.003	3	4
CNS	MYG1 →	+0.537	+0.887	<.001	.001	3	4
URINARY_TRACT	GEMIN2 →	+0.522	+1.972	<.001	<.001	3	4
LUNG_NSCLC_LUSC	SPATS2 →	+1.371	+1.115	.002	.005	3	3
LUNG_NSCLC_LUSC	MACROH2A2 →	+3.200	+1.377	.009	.001	2	4
CNS	GPR89A →	-0.441	-0.842	<.001	.002	3	3

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

RFC5 by Positive regulation of secondary metabolite biosynthetic process activity — CNS

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