Podosome assembly

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

The most reproducible pathway-associated genes across cancer lineages are GAMT, SYCE3, and TMED4, each associated with the pathway in up to 4 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, GAMT grouped by Podosome assembly-low versus -high activity in STOMACH.

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
STOMACH	GAMT →	+2.714	+0.845	.005	.008	3	4
BONE	SYCE3 →	+1.366	+2.018	.005	<.001	3	4
SOFT_TISSUE	TMED4 →	+0.766	+1.369	.001	.004	3	3
BONE	CTC1 →	+1.371	+2.018	<.001	<.001	3	3
LIVER	SPN →	+0.215	+1.875	.002	.004	3	3
BONE	NELFCD →	+0.700	+2.192	.008	<.001	3	3

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

GAMT by Podosome assembly activity — STOMACH

Explore this box plot interactively →