Negative regulation of intracellular protein transport

Across TCGA patient cohorts, RNA activity of the Negative regulation of intracellular protein transport pathway is significantly associated with the RNA expression of multiple genes, with the LSCC cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are SET, TDG, and BRCA2, 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 scatter plot shows the strongest association, Negative regulation of intracellular protein transport activity versus SET in LSCC (Pearson r = -0.20).

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
LSCC	SET →	-0.588	-0.298	<.001	<.001	3	4
LSCC	TDG →	-0.570	-0.275	<.001	.001	3	4
LSCC	BRCA2 →	-0.854	-0.329	<.001	<.001	3	4
LSCC	HCN3 →	-0.486	-0.240	.006	<.001	3	4
UCEC	H4C5 →	-1.043	-0.167	.008	.001	3	4
UCEC	H2BC7 →	-1.124	-0.177	<.001	.002	3	4

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

GO:0090317 vs SET — LSCC

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