Protein localization to chromatin

Across TCGA patient cohorts, RNA activity of the Protein localization to chromatin pathway is significantly associated with the protein abundance of multiple proteins, with the BRCA cohort showing a particularly strong set of associations.

The most reproducible pathway-associated proteins across cancer lineages are SMARCA4_S1452, SMARCA4_S1484, and SMC2, each associated with the pathway in up to 8 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, Protein localization to chromatin activity versus SMARCA4_S1452 in BRCA (Pearson r = 0.29).

Pathway-associated proteins 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 protein	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
BRCA	SMARCA4_S1452 →	+0.666	+0.045	<.001	<.001	3	8
BRCA	SMARCA4_S1484 →	+0.666	+0.045	<.001	<.001	3	8
GBM	SMC2 →	+0.693	+0.055	<.001	<.001	3	8
LUAD	TPX2_S738 →	+0.875	+0.031	<.001	<.001	3	8
GBM	VRK1 →	+0.410	+0.039	.001	.001	3	8
LUAD	CDYL_S216 →	+0.724	+0.035	<.001	<.001	3	8

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

GO:0071168 vs SMARCA4_S1452 — BRCA

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