Negative regulation of gene expression via chromosomal CpG island methylation

Across TCGA cell cohorts, RNA activity of the Negative regulation of gene expression via chromosomal CpG island methylation pathway is significantly associated with the RNA expression of multiple genes, with the SOFT_TISSUE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SAFB, UHRF1, and RAVER1, each associated with the pathway in up to 8 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, Negative regulation of gene expression via chromosomal CpG island methylation activity versus SAFB in SOFT_TISSUE (Pearson r = 0.68).

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
SOFT_TISSUE	SAFB →	+0.699	+1.047	.003	.002	3	8
SOFT_TISSUE	UHRF1 →	+1.864	+1.556	.003	<.001	3	6
SOFT_TISSUE	RAVER1 →	+1.044	+1.144	<.001	.009	3	6
SKIN	MBD3 →	+0.726	+1.092	.006	<.001	2	7
SOFT_TISSUE	EHMT2 →	+0.977	+1.216	<.001	.006	3	5
SOFT_TISSUE	SRCAP →	+1.128	+1.047	.002	.002	3	5

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

GO:0044027 vs SAFB — SOFT_TISSUE

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