Rap protein signal transduction

Across TCGA cell cohorts, RNA activity of the Rap protein signal transduction 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 YTHDF3, RAPGEFL1, and KIAA1109, each associated with the pathway in up to 8 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 scatter plot shows the strongest association, Rap protein signal transduction activity versus YTHDF3 in LARGE_INTESTINE (Pearson r = 0.35).

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	YTHDF3 →	+0.529	+0.056	.002	<.001	2	8
UPPER_AERODIGESTIVE_TRACT	RAPGEFL1 →	+1.397	+0.070	<.001	.001	3	7
STOMACH	KIAA1109 →	+0.819	+0.059	<.001	.001	3	7
STOMACH	RAPGEF6 →	+0.780	+0.073	<.001	.001	3	7
STOMACH	DMXL1 →	+0.868	+0.091	<.001	<.001	3	7
BONE	RAP2B →	+0.784	+0.077	<.001	<.001	3	7

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

GO:0032486 vs YTHDF3 — LARGE_INTESTINE

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