Neural plate pattern specification

Across TCGA cell cohorts, RNA activity of the Neural plate pattern specification pathway is significantly associated with the shRNA dependency 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 BMPR1A, CELSR2, and PTCH1, each associated with the pathway in up to 9 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, BMPR1A 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	BMPR1A →	-0.229	-0.928	.002	.003	3	9
CNS	CELSR2 →	-0.224	-0.931	<.001	<.001	3	9
CNS	PTCH1 →	-0.204	-1.182	<.001	<.001	3	5
OVARY	RASGEF1C →	-0.281	-1.021	.002	.001	3	4
BLOOD_Myeloma	ESYT2 →	-0.202	-1.898	<.001	<.001	3	4
PANCREAS	ACYP2 →	+0.278	+1.486	.001	<.001	3	4

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

BMPR1A by Neural plate pattern specification activity — LARGE_INTESTINE

Explore this box plot interactively →