Regulation of synapse pruning

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

The most reproducible pathway-associated genes across cancer lineages are CNN3P1, DIPK1A, and CSF1, each associated with the pathway in up to 3 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 CNN3P1 in GBM (Pearson r = 0.38).

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
GBM	CNN3P1 →	+0.280	+0.205	.002	<.001	3	3
OV	DIPK1A →	+0.610	+0.103	.003	.004	3	3
CCRCC	CSF1 →	+0.358	+0.391	.008	.003	3	3
CCRCC	TAP2 →	+0.322	+0.296	.001	.009	3	3
CCRCC	MIR5696 →	-0.262	-0.400	<.001	.007	3	3
CCRCC	LAG3 →	+0.720	+0.515	<.001	.001	3	3

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

GO:1905806 vs CNN3P1 — GBM

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