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 CNS cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are GGACT, CCDC103, and COX6C, each associated with the pathway in up to 5 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, GGACT grouped by Negative regulation of gene expression via chromosomal CpG island methylation-low versus -high activity in CNS.

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
CNS	GGACT →	+0.762	+0.183	.002	.005	3	5
UPPER_AERODIGESTIVE_TRACT	CCDC103 →	+0.828	+0.211	.007	.008	3	4
OVARY	COX6C →	+0.645	+0.286	.003	.003	2	5
LIVER	ATP6V1A →	-0.691	-0.246	.002	.001	3	4
LIVER	INKA2 →	-0.846	-0.327	.003	.006	3	4
LARGE_INTESTINE	WASF1 →	-0.840	-0.277	.002	.003	3	4

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

GGACT by Negative regulation of gene expression via chromosomal CpG island methylation activity — CNS

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