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 OESOPHAGUS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are CLIC3, SEC22A, and DPY19L1, 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, CLIC3 grouped by Regulation of synapse pruning-low versus -high activity in OESOPHAGUS.

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
OESOPHAGUS	CLIC3 →	+3.272	+1.041	.001	.007	3	4
STOMACH	SEC22A →	+0.708	+1.639	.001	<.001	3	4
STOMACH	DPY19L1 →	-1.421	-1.577	.004	.001	3	4
STOMACH	C6orf120 →	+0.828	+1.181	<.001	.001	3	4
STOMACH	ISG15 →	+2.304	+1.260	.009	.009	3	4
STOMACH	HACD2 →	+1.032	+1.343	.009	.002	3	4

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

CLIC3 by Regulation of synapse pruning activity — OESOPHAGUS

Explore this box plot interactively →