Low-density lipoprotein particle clearance

Across TCGA cell cohorts, RNA activity of the Low-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 CSK, ANKMY1, and HNRNPK, each associated with the pathway in up to 5 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, CSK grouped by Low-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	CSK →	-0.185	-0.596	<.001	.005	3	5
BREAST	ANKMY1 →	-0.275	-0.674	.004	.003	3	4
KIDNEY	HNRNPK →	-0.553	-1.243	.003	.002	2	5
KIDNEY	TCN2 →	-0.328	-0.981	.007	.009	3	4
URINARY_TRACT	CPA6 →	-0.260	-1.195	<.001	.005	3	4
SKIN	DNAI2 →	+0.203	+0.997	.007	.008	3	4

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

CSK by Low-density lipoprotein particle clearance activity — BREAST

Explore this box plot interactively →