RNA methylation

Across TCGA patient cohorts, RNA activity of the RNA methylation pathway is significantly associated with the RNA expression of multiple genes, with the HNSC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PLAC9, SCN2B, and NEXN, 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, RNA methylation activity versus PLAC9 in HNSC (Pearson r = -0.25).

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
HNSC	PLAC9 →	-0.899	-0.230	<.001	<.001	3	8
GBM	SCN2B →	-1.035	-0.236	<.001	<.001	3	8
OV	NEXN →	-0.915	-0.185	<.001	<.001	3	8
BRCA	LMOD1 →	-1.002	-0.264	<.001	<.001	3	8
OV	ZCCHC24 →	-1.172	-0.219	<.001	<.001	3	8
BRCA	DACT3 →	-0.823	-0.310	<.001	<.001	3	8

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

GO:0001510 vs PLAC9 — HNSC

Explore this scatter interactively →