Methylation

Across TCGA patient cohorts, RNA activity of the Methylation pathway is significantly associated with the protein abundance of multiple proteins, with the LSCC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are TRIM28, PUF60, and RPRD2, 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, Methylation activity versus TRIM28 in LSCC (Pearson r = 0.36).

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
LSCC	TRIM28 →	+0.370	+0.032	<.001	<.001	3	8
PDAC	PUF60 →	+0.208	+0.019	.001	<.001	3	8
HNSC	RPRD2 →	+0.229	+0.063	<.001	<.001	3	7
LSCC	SMC3 →	+0.235	+0.026	<.001	<.001	3	7
LSCC	ADNP →	+0.301	+0.026	<.001	<.001	3	7
HNSC	CPSF6 →	+0.252	+0.053	<.001	.002	3	7

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

GO:0032259 vs TRIM28 — LSCC

Explore this scatter interactively →