Regulation of synapse pruning

Across TCGA cell cohorts, RNA activity of the Regulation of synapse pruning pathway is significantly associated with the RNA expression of multiple genes, with the CNS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are NLGN4Y, PPM1A, and TRIM3, each associated with the pathway in up to 2 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 scatter plot shows the strongest association, Regulation of synapse pruning activity versus NLGN4Y in CNS (Pearson r = 0.85).

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
CNS	NLGN4Y →	+2.630	+0.205	.005	.007	3	2
CNS	PPM1A →	+0.810	+0.205	.006	.007	3	1
CNS	TRIM3 →	+0.858	+0.205	.003	.007	3	1
CNS	SMOC2 →	+0.097	+0.205	<.001	.007	3	1
CNS	KLK8 →	+0.310	+0.205	.003	.007	3	1
CNS	CMPK2 →	+1.089	+0.205	.008	.007	3	1

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

GO:1905806 vs NLGN4Y — CNS

Explore this scatter interactively →