DNA topological change

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

The most reproducible pathway-associated genes across cancer lineages are PHF20, KNTC1, and ATP7A, each associated with the pathway in up to 4 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, PHF20 grouped by DNA topological change-low versus -high activity in BLOOD_Myeloma.

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_Myeloma	PHF20 →	-0.623	-0.491	.003	.007	3	4
LUNG_SCLC	KNTC1 →	+1.043	+0.408	.001	.001	3	4
LIVER	ATP7A →	-1.195	-0.291	.006	.009	3	4
LUNG_NSCLC_LUSC	AASDH →	-0.547	-0.240	.004	<.001	2	4
BREAST	TTC25 →	-0.405	-0.399	.003	.005	3	3
BLOOD_Lymphoma	KIAA0232 →	-0.966	-0.480	<.001	<.001	3	3

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

PHF20 by DNA topological change activity — BLOOD_Myeloma

Explore this box plot interactively →