COPII-coated vesicle cargo loading

Across TCGA cell cohorts, RNA activity of the COPII-coated vesicle cargo loading 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 SCAP, SEC13, and CCNJL, each associated with the pathway in up to 10 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, SCAP grouped by COPII-coated vesicle cargo loading-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	SCAP →	-0.611	-0.391	<.001	<.001	3	10
OESOPHAGUS	SEC13 →	-0.610	-0.320	<.001	.002	3	9
CNS	CCNJL →	-0.273	-1.162	.003	.008	3	5
SKIN	MAP7D1 →	-0.219	-0.325	.001	.008	3	4
LARGE_INTESTINE	OR5AU1 →	+0.161	+0.260	.007	.001	3	4
LUNG_NSCLC_LUSC	TRAF3 →	-0.265	-0.216	<.001	<.001	3	4

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

SCAP by COPII-coated vesicle cargo loading activity — LARGE_INTESTINE

Explore this box plot interactively →