Secondary palate development

Across TCGA cell cohorts, RNA activity of the Secondary palate development 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 USP28, SDC4, and TWNK, 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, USP28 grouped by Secondary palate development-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	USP28 →	+1.066	+0.270	.001	.003	3	5
KIDNEY	SDC4 →	-1.033	-0.707	.003	.001	3	4
LARGE_INTESTINE	TWNK →	+0.536	+0.648	.001	.002	3	4
LUNG_NSCLC_LUSC	OTX1 →	+1.460	+0.377	.001	.009	3	3
BONE	SENP5 →	-0.676	-0.418	.004	.009	3	3
OVARY	EIF3A →	+0.515	+0.452	<.001	.005	3	3

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

USP28 by Secondary palate development activity — OESOPHAGUS

Explore this box plot interactively →