Synaptonemal complex organization

Across TCGA cell cohorts, RNA activity of the Synaptonemal complex organization pathway is significantly associated with the shRNA dependency of multiple genes, with the BONE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are GLI2, SIRT5, and WDR59, 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, GLI2 grouped by Synaptonemal complex organization-low versus -high activity in BONE.

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
BONE	GLI2 →	-0.230	-0.236	.008	.005	3	4
LIVER	SIRT5 →	-0.245	-0.194	.002	<.001	3	4
BLOOD_Lymphoma	WDR59 →	-0.316	-0.264	.007	<.001	2	5
LARGE_INTESTINE	ZNF606 →	+0.290	+0.169	<.001	.001	3	4
STOMACH	HRH3 →	+0.645	+0.296	.002	<.001	3	4
STOMACH	APOC4-APOC2 →	+0.097	+0.223	.003	.002	3	4

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

GLI2 by Synaptonemal complex organization activity — BONE

Explore this box plot interactively →