Negative regulation of gene expression via chromosomal CpG island methylation

Across TCGA patient cohorts, RNA activity of the Negative regulation of gene expression via chromosomal CpG island methylation pathway is significantly associated with the protein abundance of multiple proteins, with the GBM cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are SMC4, TOP2A, and XRCC1_S241, 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, Negative regulation of gene expression via chromosomal CpG island methylation activity versus SMC4 in GBM (Pearson r = 0.56).

Pathway-associated proteins 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 protein	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
GBM	SMC4 →	+0.673	+0.067	<.001	<.001	3	9
UCEC	TOP2A →	+0.828	+0.078	.002	<.001	3	9
LUAD	XRCC1_S241 →	+0.715	+0.076	.001	<.001	3	8
BRCA	SETDB1_S1066 →	+0.906	+0.056	<.001	<.001	3	8
GBM	SMC2 →	+0.737	+0.072	<.001	<.001	3	8
GBM	BAZ1B →	+0.384	+0.086	<.001	<.001	3	8

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

GO:0044027 vs SMC4 — GBM

Explore this scatter interactively →