Indole-containing compound biosynthetic process

Across TCGA cell cohorts, RNA activity of the Indole-containing compound biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the SOFT_TISSUE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are CLIC1, PITX1, and ZBTB10, 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, CLIC1 grouped by Indole-containing compound biosynthetic process-low versus -high activity in SOFT_TISSUE.

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
SOFT_TISSUE	CLIC1 →	+1.094	+1.318	.002	.001	3	4
SOFT_TISSUE	PITX1 →	+2.716	+1.709	.001	<.001	3	4
LUNG_NSCLC_LUSC	ZBTB10 →	+1.386	+1.381	.001	.002	3	4
CNS	SCN11A →	-0.013	-1.066	.001	.002	3	4
BLOOD_Leukemia	STARD13 →	+1.202	+1.319	.006	.002	3	4
LUNG_NSCLC_LUAD	FIG4 →	+0.573	+0.998	.001	.004	3	4

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

CLIC1 by Indole-containing compound biosynthetic process activity — SOFT_TISSUE

Explore this box plot interactively →