SMCHD1

Across TCGA cell cohorts, SMCHD1 mutation is significantly associated with the mutation status of many other genes, with 6,164 significant associations in total. LARGE_INTESTINE shows the largest number of these associations.

The most reproducible SMCHD1-associated genes across cancer lineages are ARID1A, NLGN2, and DPYSL3. Each is linked with SMCHD1 in more than 4 cancer types. Because this analysis shows association rather than direction, both SMCHD1-to-partner and partner-to-SMCHD1 results are reported.

Each partner links to its own Q-omics profile. The box plot shows the strongest example, ARID1A grouped by SMCHD1-low versus SMCHD1-high in CNS.

mutation associated genes by consensus

Ranked by combined sampling and lineage consensus. X-score (SMCHD1→partner) and Y-score (partner→SMCHD1) are standardized regression coefficients; both directions are reported because the association is undirected. p-values are from the association test.

Lineage	Partner gene	X-score	Y-score	p(X)	p(Y)	Sampling consensus	Lineage consensus
CNS	ARID1A →	+3.541	+4.139	.003	.003	1	5
BLOOD_Leukemia	NLGN2 →	+4.662	+3.963	<.001	<.001	1	5
BLOOD_Lymphoma	DPYSL3 →	+4.584	+4.584	.007	.007	1	5
BLOOD_Leukemia	SPEN →	+2.160	+3.120	.001	.001	1	5
LARGE_INTESTINE	PRR12 →	+1.860	+2.263	.002	.002	1	5
LARGE_INTESTINE	AFF3 →	+2.374	+2.604	<.001	<.001	1	5

Each partner links to its Q-omics profile. Showing the 6 strongest of 6,164 associations by consensus.

ARID1A by SMCHD1 expression — CNS

Explore this box plot interactively →