Enhancing cancer clonality analysis with integrative genomics

BMC Bioinformatics

Table 5 DNA methylation of TSGs in the Presentation sample

Target ID	Avg-Beta	Gene	Ensembl GeneID	RNA Read Count	Classification	Regulatory Feature	Relation to CpG Island
cg27549619	0.3934072	AXIN1	ENSG00000103126	4	TSG	Promoter Associated	Island
cg26370022	0.6804651	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg11529738	0.7789396	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg24900425	0.9020266	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg13601799	0.2905587	CDKN2A	ENSG00000147889	13	TSG	Promoter Associated	Island
cg01437571	0.3243266	CEBPA	ENSG00000245848	0	TSG	Promoter Associated	Island
cg00976692	0.291538	MEN1	ENSG00000133895	8	TSG	Promoter Associated	Island
cg14803009	0.3387372	MSH2	ENSG00000095002	0	TSG	Promoter Associated	Island
cg22866426	0.4628801	RUNX1	ENSG00000159216	1	TSG	Promoter Associated	Island
cg27003951	0.2562254	SOCS1	ENSG00000185338	0	TSG	Promoter Associated	Island

Listed are the DNA methylation of tumor suppressor genes (TSGs) passing iCloneViz filtering criteria from ~485,000 possible candidates, for the Presentation sample. The filtering criteria consisted of: i) Avg-Beta ≥ 25%, ii) "Promoter Associated" regulatory feature, and iii) being from a CpG Island. The methylation data set was integrated with RNA-seq to directly associate the raw (unnormalized) RNA Read Counts for the identified TSGs.

ISSN: 1471-2105