Positive regulation of chromosome organization

Across TCGA patient cohorts, RNA activity of the Positive regulation of chromosome organization 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 HPGDS, TOMM40, and NPTN, each associated with the pathway in up to 3 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, Positive regulation of chromosome organization activity versus HPGDS in BRCA (Pearson r = -0.47).

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	HPGDS →	-1.124	-0.390	.002	.009	3	3
OV	TOMM40 →	+0.626	+0.142	<.001	.003	3	2
OV	NPTN →	-0.553	-0.136	.007	.003	2	3
BRCA	CX3CR1 →	-1.791	-0.379	.002	.008	3	2
BRCA	GCSAML →	-1.005	-0.445	.004	.005	2	3
BRCA	DNM3OS →	-1.632	-0.400	.002	.004	3	2

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

GO:2001252 vs HPGDS — BRCA

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