Regulation of high-density lipoprotein particle clearance

Across TCGA cell cohorts, RNA activity of the Regulation of high-density lipoprotein particle clearance pathway is significantly associated with the shRNA dependency of multiple genes, with the BREAST cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are AK3, ZYX, and ARF4, 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, AK3 grouped by Regulation of high-density lipoprotein particle clearance-low versus -high activity in BREAST.

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
BREAST	AK3 →	+0.200	+0.829	.001	.005	3	4
STOMACH	ZYX →	-0.198	-1.536	.003	<.001	3	4
LUNG_NSCLC_LUAD	ARF4 →	-0.292	-1.097	.004	<.001	3	4
LUNG_NSCLC_LUAD	PPP1CB →	+0.308	+0.863	<.001	<.001	3	4
PANCREAS	NFATC3 →	-0.199	-1.585	.001	<.001	3	4
UPPER_AERODIGESTIVE_TRACT	TESK1 →	-0.126	-1.738	.002	<.001	3	3

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

AK3 by Regulation of high-density lipoprotein particle clearance activity — BREAST

Explore this box plot interactively →