Chondroitin sulfate proteoglycan biosynthetic process

Across TCGA cell cohorts, RNA activity of the Chondroitin sulfate proteoglycan biosynthetic process 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 PNPT1, EYS, and FABP6, 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, PNPT1 grouped by Chondroitin sulfate proteoglycan biosynthetic process-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	PNPT1 →	-0.514	-0.099	.002	.001	3	4
LARGE_INTESTINE	EYS →	-0.178	-0.074	.009	.001	3	4
SOFT_TISSUE	FABP6 →	+0.195	+0.145	.008	<.001	3	4
SOFT_TISSUE	SPSB4 →	+0.258	+0.160	.005	.003	3	4
KIDNEY	CYB561A3 →	-0.205	-0.109	.001	.001	3	4
LUNG_NSCLC_LUSC	RHOQ →	+0.224	+0.134	.004	.002	3	4

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

PNPT1 by Chondroitin sulfate proteoglycan biosynthetic process activity — LARGE_INTESTINE

Explore this box plot interactively →