Secondary metabolic process

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

The most reproducible pathway-associated genes across cancer lineages are NEFH, CBR4, and CNN1, each associated with the pathway in up to 7 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, NEFH grouped by Secondary metabolic process-low versus -high activity in STOMACH.

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
STOMACH	NEFH →	-0.407	-1.408	.001	<.001	3	6
BLOOD_Leukemia	CBR4 →	-0.263	-0.942	.004	.004	2	7
BREAST	CNN1 →	-0.156	-0.765	<.001	.003	3	5
LARGE_INTESTINE	TMX2 →	-0.200	-1.233	<.001	<.001	3	5
SKIN	CYP51A1 →	-0.148	-1.066	<.001	<.001	3	4
BLOOD_Lymphoma	KRT85 →	-0.265	-1.099	<.001	.008	3	4

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

NEFH by Secondary metabolic process activity — STOMACH

Explore this box plot interactively →