R-loop processing

Across TCGA cell cohorts, RNA activity of the R-loop processing pathway is significantly associated with the RNA expression of multiple genes, with the LIVER cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are CEP57, WDR41, and KLHL5, 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 scatter plot shows the strongest association, R-loop processing activity versus CEP57 in LIVER (Pearson r = 0.73).

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
LIVER	CEP57 →	+0.960	+0.268	.009	.005	3	5
STOMACH	WDR41 →	-0.696	-0.233	.009	.009	3	4
BONE	KLHL5 →	-2.462	-0.280	<.001	.002	3	4
BONE	LEPROT →	-1.376	-0.276	<.001	.002	3	4
BONE	MECOM →	-2.298	-0.254	<.001	.004	3	4
LUNG_SCLC	RAB29 →	-0.951	-0.174	<.001	.003	3	4

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

GO:0062176 vs CEP57 — LIVER

Explore this scatter interactively →