Regulation of apoptotic cell clearance

Across TCGA cell cohorts, RNA activity of the Regulation of 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 HMGB1, CCL2, and TIMM50, each associated with the pathway in up to 11 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, HMGB1 grouped by Regulation of 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	HMGB1 →	-0.343	-0.967	<.001	<.001	3	11
SKIN	CCL2 →	-0.186	-1.190	.002	<.001	2	8
CNS	TIMM50 →	-0.206	-0.915	<.001	.002	3	5
CNS	TREM2 →	-0.168	-0.900	.003	.003	3	5
BLOOD_Lymphoma	JPH4 →	+0.202	+1.350	.002	.009	3	5
CNS	MGRN1 →	-0.268	-1.207	<.001	<.001	3	4

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

HMGB1 by Regulation of apoptotic cell clearance activity — LARGE_INTESTINE

Explore this box plot interactively →