Synapse pruning

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

The most reproducible pathway-associated genes across cancer lineages are PLPP7, DNAJB6, and FBXW7, 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, PLPP7 grouped by Synapse pruning-low versus -high activity in KIDNEY.

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
KIDNEY	PLPP7 →	-0.200	-0.176	<.001	<.001	3	5
OVARY	DNAJB6 →	+0.186	+0.229	.002	.008	3	5
SOFT_TISSUE	FBXW7 →	-0.295	-0.270	.001	.002	3	4
KIDNEY	MTUS2 →	+0.288	+0.225	.001	<.001	2	5
OVARY	HES4 →	-0.244	-0.244	<.001	.003	3	4
OVARY	GJB3 →	-0.127	-0.199	.003	.002	3	4

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

PLPP7 by Synapse pruning activity — KIDNEY

Explore this box plot interactively →