DNA cytosine deamination

Across TCGA cell cohorts, RNA activity of the DNA cytosine deamination pathway is significantly associated with the RNA expression of multiple genes, with the OESOPHAGUS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are CDK5RAP3, HS6ST2, and SMPDL3A, 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, CDK5RAP3 grouped by DNA cytosine deamination-low versus -high activity in OESOPHAGUS.

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
OESOPHAGUS	CDK5RAP3 →	+1.019	+1.387	.002	<.001	3	5
BREAST	HS6ST2 →	+1.827	+0.981	<.001	.002	3	5
KIDNEY	SMPDL3A →	-1.891	-1.393	.002	<.001	3	5
KIDNEY	NDUFA4 →	-0.831	-1.335	.007	<.001	3	5
BONE	FBXO6 →	-2.230	-1.505	<.001	.004	3	4
BONE	ZNF711 →	-0.859	-1.640	.005	.001	3	4

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

CDK5RAP3 by DNA cytosine deamination activity — OESOPHAGUS

Explore this box plot interactively →