PML body organization

Across TCGA cell cohorts, RNA activity of the PML body organization pathway is significantly associated with the shRNA dependency of multiple genes, with the BONE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are EPB41L4B, FKBP9P1, and MSL3, 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 box plot shows the strongest association, EPB41L4B grouped by PML body organization-low versus -high activity in BONE.

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
BONE	EPB41L4B →	-0.258	-0.197	.005	.005	3	5
LUNG_NSCLC_LUSC	FKBP9P1 →	-0.203	-0.190	<.001	.002	3	5
URINARY_TRACT	MSL3 →	-0.518	-0.182	.001	.002	3	5
LUNG_NSCLC_LUSC	MYBL2 →	-0.558	-0.206	.002	<.001	3	5
BREAST	SOHLH1 →	+0.164	+0.140	<.001	.003	3	5
URINARY_TRACT	NCS1 →	+0.186	+0.188	.003	.001	3	5

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

EPB41L4B by PML body organization activity — BONE

Explore this box plot interactively →