Autophagosome maturation

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

The most reproducible pathway-associated genes across cancer lineages are VCP, GRK3, and SNU13, each associated with the pathway in up to 6 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, VCP grouped by Autophagosome maturation-low versus -high activity in SKIN.

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
SKIN	VCP →	-0.847	-0.279	.004	.004	2	6
LARGE_INTESTINE	GRK3 →	+0.262	+0.200	.001	.002	3	5
LARGE_INTESTINE	SNU13 →	+0.218	+0.315	.002	<.001	3	5
BREAST	HGS →	-0.558	-0.260	<.001	<.001	3	5
LIVER	TSG101 →	-0.533	-0.271	.001	.007	3	5
KIDNEY	GGT3P →	-0.277	-0.428	<.001	.007	3	5

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

VCP by Autophagosome maturation activity — SKIN

Explore this box plot interactively →