Neural plate pattern specification

Across TCGA cell cohorts, RNA activity of the Neural plate pattern specification pathway is significantly associated with the RNA expression of multiple genes, with the LARGE_INTESTINE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are RAVER2, GFOD2, and GGA2, 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, RAVER2 grouped by Neural plate pattern specification-low versus -high activity in LARGE_INTESTINE.

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
LARGE_INTESTINE	RAVER2 →	-0.852	-0.867	.003	.002	3	4
SOFT_TISSUE	GFOD2 →	-0.651	-1.259	.007	<.001	3	4
BLOOD_Leukemia	GGA2 →	-1.353	-1.421	.002	<.001	3	3
BLOOD_Leukemia	WNK4 →	+0.683	+0.961	.003	.004	3	3
BLOOD_Leukemia	STAT6 →	-1.069	-1.301	<.001	.001	3	3
BLOOD_Leukemia	TNS1 →	-1.806	-1.101	<.001	<.001	3	3

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

RAVER2 by Neural plate pattern specification activity — LARGE_INTESTINE

Explore this box plot interactively →