Pyrimidine nucleobase biosynthetic process

Across TCGA cell cohorts, RNA activity of the Pyrimidine nucleobase biosynthetic process pathway is significantly associated with the RNA expression of multiple genes, with the UPPER_AERODIGESTIVE_TRACT cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are VGLL4, TIMP1, and ZBED3, 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, Pyrimidine nucleobase biosynthetic process activity versus VGLL4 in UPPER_AERODIGESTIVE_TRACT (Pearson r = 0.68).

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
UPPER_AERODIGESTIVE_TRACT	VGLL4 →	+0.852	+1.325	<.001	.003	3	6
BLOOD_Leukemia	TIMP1 →	-2.121	-0.252	<.001	<.001	3	5
BLOOD_Leukemia	ZBED3 →	+1.050	+0.276	.003	.003	3	5
KIDNEY	PHYKPL →	+1.378	+0.311	<.001	<.001	3	5
LARGE_INTESTINE	FPR1 →	-0.254	-0.875	.007	<.001	3	5
PANCREAS	TUBG1 →	+0.853	+1.137	<.001	<.001	3	5

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

GO:0019856 vs VGLL4 — UPPER_AERODIGESTIVE_TRACT

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