Convergent extension

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

The most reproducible pathway-associated genes across cancer lineages are RNFT1, CITED1, and SEMA4D, 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, RNFT1 grouped by Convergent extension-low versus -high activity in SKIN.

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
SKIN	RNFT1 →	-0.737	-1.229	.008	.003	3	4
LUNG_SCLC	CITED1 →	+2.285	+1.749	.007	<.001	3	3
CNS	SEMA4D →	+1.658	+2.003	.002	<.001	3	3
CNS	NHSL2 →	+1.145	+2.245	.002	.003	2	4
STOMACH	FBXO33 →	+0.835	+1.624	.001	.007	3	3
KIDNEY	LDHA →	+0.935	+1.810	.004	<.001	3	3

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

RNFT1 by Convergent extension activity — SKIN

Explore this box plot interactively →