Indole-containing compound metabolic process

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

The most reproducible pathway-associated genes across cancer lineages are ATPAF1, SART3, and TRAPPC10, 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, ATPAF1 grouped by Indole-containing compound metabolic process-low versus -high activity in BLOOD_Lymphoma.

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
BLOOD_Lymphoma	ATPAF1 →	+0.206	+1.918	<.001	<.001	3	3
UPPER_AERODIGESTIVE_TRACT	SART3 →	+0.306	+0.288	<.001	.003	3	3
BLOOD_Myeloma	TRAPPC10 →	+0.267	+0.306	.006	.005	2	4
LARGE_INTESTINE	MRRF →	-0.145	-0.894	.007	.007	3	2
LARGE_INTESTINE	UBE3B →	+0.153	+0.687	<.001	.003	3	2
OVARY	TADA2B →	-0.330	-0.309	.009	.007	3	2

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

ATPAF1 by Indole-containing compound metabolic process activity — BLOOD_Lymphoma

Explore this box plot interactively →