Protein-DNA covalent cross-linking repair

Across TCGA cell cohorts, RNA activity of the Protein-DNA covalent cross-linking repair pathway is significantly associated with the shRNA dependency of multiple genes, with the BREAST cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SLC36A1, PPP4R3B, and DNAJC5, each associated with the pathway in up to 4 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, SLC36A1 grouped by Protein-DNA covalent cross-linking repair-low versus -high activity in BREAST.

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
BREAST	SLC36A1 →	+0.430	+0.151	<.001	<.001	3	4
BLOOD_Lymphoma	PPP4R3B →	+0.459	+0.221	.002	.005	3	3
BREAST	DNAJC5 →	+0.131	+0.101	.005	.004	3	3
BREAST	MTG1 →	+0.218	+0.236	.002	<.001	3	3
BREAST	VCP →	-0.503	-0.126	<.001	<.001	3	3
SKIN	COL1A1 →	+0.147	+0.197	.005	<.001	3	3

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

SLC36A1 by Protein-DNA covalent cross-linking repair activity — BREAST

Explore this box plot interactively →