Formation of primary germ layer

Across TCGA cell cohorts, RNA activity of the Formation of primary germ layer pathway is significantly associated with the shRNA dependency of multiple genes, with the CNS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PDE6G, OMD, and SLC38A3, 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, PDE6G grouped by Formation of primary germ layer-low versus -high activity in CNS.

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
CNS	PDE6G →	-0.177	-0.099	<.001	<.001	3	5
LUNG_SCLC	OMD →	-0.365	-0.120	.001	.004	3	4
SKIN	SLC38A3 →	-0.263	-0.098	.004	.005	3	4
SKIN	PMS2P9 →	+0.162	+0.111	.001	<.001	3	4
STOMACH	CCDC71 →	+0.225	+0.112	.001	.001	3	4
STOMACH	TBX5 →	-0.110	-0.089	.007	<.001	3	4

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

PDE6G by Formation of primary germ layer activity — CNS

Explore this box plot interactively →