mRNA 3'-splice site recognition

Across TCGA cell cohorts, RNA activity of the mRNA 3'-splice site recognition pathway is significantly associated with the RNA expression of multiple genes, with the KIDNEY cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SETD2, SMARCC1, and FANCA, each associated with the pathway in up to 6 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, mRNA 3'-splice site recognition activity versus SETD2 in KIDNEY (Pearson r = 0.80).

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
KIDNEY	SETD2 →	+1.154	+0.172	.006	.007	3	6
BONE	SMARCC1 →	+1.421	+0.177	.001	.007	3	6
KIDNEY	FANCA →	+1.767	+0.187	<.001	.004	3	5
KIDNEY	SPINDOC →	+1.125	+0.180	.001	.004	3	5
BONE	ACTR3B →	+1.589	+0.143	<.001	.003	3	5
BLOOD_Lymphoma	ILF3 →	+0.844	+0.081	<.001	.002	3	5

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

GO:0000389 vs SETD2 — KIDNEY

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