Negative regulation of secondary metabolite biosynthetic process

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

The most reproducible pathway-associated genes across cancer lineages are OPN3, SLC24A5, and RAPGEF2, each associated with the pathway in up to 13 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, OPN3 grouped by Negative regulation of secondary metabolite biosynthetic process-low versus -high activity in LIVER.

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
LIVER	OPN3 →	-0.374	-2.054	<.001	<.001	3	13
CNS	SLC24A5 →	-0.330	-1.480	<.001	<.001	3	8
KIDNEY	RAPGEF2 →	-0.285	-1.118	.005	.008	3	7
LUNG_NSCLC_LUAD	WNT5A →	-0.138	-1.303	<.001	<.001	3	6
BLOOD_Lymphoma	CUTC →	-0.341	-2.423	.003	<.001	3	5
LIVER	CD3G →	+0.345	+1.903	.009	<.001	3	4

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

OPN3 by Negative regulation of secondary metabolite biosynthetic process activity — LIVER

Explore this box plot interactively →