DNA methylation-dependent heterochromatin formation

Across TCGA cell cohorts, RNA activity of the DNA methylation-dependent heterochromatin formation pathway is significantly associated with the RNA expression of multiple genes, with the LUNG_SCLC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are NUDT6, SH3BP2, and ATG10, 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, NUDT6 grouped by DNA methylation-dependent heterochromatin formation-low versus -high activity in LUNG_SCLC.

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
LUNG_SCLC	NUDT6 →	-0.750	-0.213	.001	.004	2	4
KIDNEY	SH3BP2 →	+1.717	+0.581	<.001	.004	3	3
LUNG_NSCLC_LUAD	ATG10 →	-0.597	-0.499	.001	.006	3	3
LUNG_NSCLC_LUAD	PTCD2 →	-0.464	-0.341	<.001	.007	3	3
LUNG_NSCLC_LUSC	POLR3A →	+0.836	+0.390	.002	.002	2	4
SKIN	CLU →	-1.751	-0.385	<.001	.006	3	3

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

NUDT6 by DNA methylation-dependent heterochromatin formation activity — LUNG_SCLC

Explore this box plot interactively →