DNA methylation-dependent heterochromatin formation

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

The most reproducible pathway-associated genes across cancer lineages are RFC3, SASS6, and FAM72B, each associated with the pathway in up to 9 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 methylation-dependent heterochromatin formation activity versus RFC3 in LSCC (Pearson r = 0.30).

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
LSCC	RFC3 →	+0.592	+0.221	<.001	.002	3	9
BRCA	SASS6 →	+0.619	+0.269	<.001	<.001	3	9
BRCA	FAM72B →	+0.839	+0.219	<.001	<.001	3	9
GBM	NCAPG →	+1.250	+1.161	<.001	<.001	3	8
GBM	FOXM1 →	+1.021	+1.058	.001	<.001	3	8
UCEC	NEK2 →	+1.040	+0.465	<.001	<.001	3	8

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

GO:0006346 vs RFC3 — LSCC

Explore this scatter interactively →