Chromatin looping

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

The most reproducible pathway-associated genes across cancer lineages are DDX39A, FCGR2A, and CENPK, 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, Chromatin looping activity versus DDX39A in BRCA (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
BRCA	DDX39A →	+0.506	+0.525	<.001	.003	3	5
BRCA	FCGR2A →	-0.495	-0.618	.001	.004	3	5
LSCC	CENPK →	+0.476	+0.658	.007	<.001	3	5
LSCC	THOP1 →	+0.529	+0.685	<.001	.002	3	5
LSCC	KNTC1 →	+0.577	+0.987	<.001	<.001	3	5
CCRCC	GLUL →	-0.708	-0.936	.003	<.001	3	4

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

GO:0140588 vs DDX39A — BRCA

Explore this scatter interactively →