Retrotransposon silencing by heterochromatin formation

Across TCGA pan-cancer cohorts, RNA activity of the Retrotransposon silencing by heterochromatin formation pathway is associated with patient survival in 24 of 34 cancer lineages. Pathway activity is summarized from the expression of its 15 member genes.

The strongest signal is observed in acute myeloid leukemia (LAML), where higher Retrotransposon silencing by heterochromatin formation pathway activity is associated with better disease-free survival. In most high-consensus cancer types, elevated pathway activity shows an unfavorable survival association, although some cancer types, such as LAML and UVM, show the opposite pattern, with higher activity associated with better survival.

LAML, LGG, and UVM are the cancer lineages in which this pathway most reproducibly stratifies patient survival.

Pathway-activity survival associations by lineage

Ranked by sampling consensus. AUC1 and AUC2 represent the survival AUCs for the high- and low-pathway-activity groups, respectively. The group with the lower AUC is interpreted as having poorer survival. The reported p-values are derived from the log-rank test.

Lineage	Measure	Split	Stage	AUC1 high	AUC2 low	p	Sampling consensus
LAML	DFS	Quartile	All	0.772	0.460	<.001	32	view →
LGG	DFS	Tertile	All	0.211	0.569	<.001	32	view →
UVM	DFS	Quartile	II,III,IV	0.757	0.260	.006	32	view →
KIRC	DFS	Quartile	IV	0.320	0.785	<.001	30	view →
THCA	DFS	Median	All	0.864	0.953	.011	22	view →
ACC	OS	Tertile	II,III,IV	0.598	0.939	.008	21	view →
KIRP	DFS	Tertile	IV	0.546	0.864	.010	17	view →
ESCA	OS	Tertile	III,IV	0.367	0.684	.012	17	view →
READ	OS	Median	IV	1.000	0.706	.007	16	view →
CHOL	OS	Quartile	All	0.840	0.348	.007	14	view →
SKCM	OS	Quartile	All	0.259	0.373	.019	11	view →
KICH	DFS	Median	All	0.671	1.000	.004	10	view →

Pink = unfavorable, green = favorable. Showing the 12 strongest of 24 lineages.

GO:0141005–LAML (DFS)

Open the LAML breakdown →