Defense response to Gram-negative bacterium

Across TCGA cell cohorts, RNA activity of the Defense response to Gram-negative bacterium pathway is significantly associated with the RNA expression of multiple genes, with the SOFT_TISSUE cohort showing a particularly strong set of associations.

The most reproducible pathway-associated genes across cancer lineages are PPM1D, GALNT6, and HMGB2, 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 scatter plot shows the strongest association, Defense response to Gram-negative bacterium activity versus PPM1D in SOFT_TISSUE (Pearson r = 0.75).

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
SOFT_TISSUE	PPM1D →	+0.950	+0.267	.004	.003	3	5
SOFT_TISSUE	GALNT6 →	-3.536	-0.222	<.001	.006	3	5
BREAST	HMGB2 →	+0.776	+0.167	.001	<.001	3	5
BLOOD_Leukemia	PDRG1 →	-0.553	-0.226	.003	.008	3	5
OVARY	NAALADL2 →	-1.261	-0.343	<.001	<.001	3	4
CNS	TGFB1 →	-1.041	-0.204	.005	.009	3	4

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

GO:0050829 vs PPM1D — SOFT_TISSUE

Explore this scatter interactively →