Secondary metabolic process

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

The most reproducible pathway-associated genes across cancer lineages are EIF3I, GNL2, and SEMA3B, each associated with the pathway in up to 4 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, EIF3I grouped by Secondary metabolic process-low versus -high activity in LUNG_SCLC.

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
LUNG_SCLC	EIF3I →	+0.685	+0.876	<.001	.009	3	4
BONE	GNL2 →	+0.856	+1.360	.002	.002	3	4
PANCREAS	SEMA3B →	-2.842	-1.023	.002	.004	3	4
BREAST	SF3B3 →	+0.571	+0.739	.003	<.001	3	4
PANCREAS	NIP7 →	+0.594	+0.711	.002	.004	3	4
URINARY_TRACT	PDLIM5 →	-1.389	-1.872	<.001	<.001	3	3

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

EIF3I by Secondary metabolic process activity — LUNG_SCLC

Explore this box plot interactively →