Synapse pruning

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

The most reproducible pathway-associated genes across cancer lineages are FEM1A, RTKN, and DARS2, 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, FEM1A grouped by Synapse pruning-low versus -high activity in UPPER_AERODIGESTIVE_TRACT.

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
UPPER_AERODIGESTIVE_TRACT	FEM1A →	+0.493	+1.221	.001	.001	3	5
LUNG_SCLC	RTKN →	+1.499	+1.177	.002	.003	3	4
BLOOD_Leukemia	DARS2 →	+0.687	+0.875	.001	<.001	3	4
LIVER	RCOR2 →	+1.901	+1.301	.001	.003	3	4
OESOPHAGUS	C2orf49 →	+1.061	+1.237	<.001	<.001	3	4
BLOOD_Leukemia	STARD5 →	+1.223	+1.097	.006	<.001	3	4

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

FEM1A by Synapse pruning activity — UPPER_AERODIGESTIVE_TRACT

Explore this box plot interactively →