Apoptotic cell clearance

Across TCGA cell cohorts, RNA activity of the Apoptotic cell clearance pathway is significantly associated with the shRNA dependency of multiple genes, with the LARGE_INTESTINE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are RAC1, PPP3R2, and PPP4C, each associated with the pathway in up to 8 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, RAC1 grouped by Apoptotic cell clearance-low versus -high activity in LARGE_INTESTINE.

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
LARGE_INTESTINE	RAC1 →	+0.697	+0.178	<.001	<.001	3	8
STOMACH	PPP3R2 →	+0.171	+0.129	.005	.004	3	7
CNS	PPP4C →	-0.297	-0.128	.001	.006	3	6
BLOOD_Leukemia	CPA6 →	-0.195	-0.147	.003	<.001	3	6
LUNG_SCLC	RPN2 →	+0.475	+0.208	.001	<.001	3	6
LARGE_INTESTINE	TLN1 →	+0.346	+0.138	.004	.003	1	8

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

RAC1 by Apoptotic cell clearance activity — LARGE_INTESTINE

Explore this box plot interactively →