DNA alkylation repair

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

The most reproducible pathway-associated genes across cancer lineages are FNDC3B, NUBP2, and USP7, 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, DNA alkylation repair activity versus FNDC3B in BLOOD_Leukemia (Pearson r = -0.55).

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
BLOOD_Leukemia	FNDC3B →	-1.345	-0.800	<.001	<.001	3	6
BLOOD_Leukemia	NUBP2 →	+0.361	+0.635	.007	.006	3	6
BLOOD_Leukemia	USP7 →	+0.848	+0.858	<.001	<.001	3	6
BLOOD_Leukemia	ARSB →	-0.742	-0.627	.001	.001	3	6
BONE	TFAP4 →	+1.084	+1.313	.003	<.001	3	6
BONE	METTL22 →	+1.372	+1.527	.007	<.001	3	5

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

GO:0006307 vs FNDC3B — BLOOD_Leukemia

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