Enhancing cancer clonality analysis with integrative genomics

BMC Bioinformatics

Table 6 DNA methylation of TSGs in the Relapse sample

Target ID	Avg-Beta	Gene	Ensembl Gene ID	RNA Read Count	Classification	Regulatory Feature	Relation to CpG Island
cg27549619	0.443731	AXIN1	ENSG00000103126	0	TSG	Promoter Associated	Island
cg02086790	0.4921295	AXIN1	ENSG00000103126	0	TSG	Promoter Associated	Island
cg26370022	0.6747859	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg24900425	0.8910863	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg11529738	0.7637555	BRCA1	ENSG00000012048	0	TSG	Promoter Associated	Island
cg13601799	0.467826	CDKN2A	ENSG00000147889	38	TSG	Promoter Associated	Island
cg00976692	0.293402	MEN1	ENSG00000133895	0	TSG	Promoter Associated	Island
cg14803009	0.4267139	MSH2	ENSG00000095002	0	TSG	Promoter Associated	Island
cg22073802	0.2875548	PTCH1	ENSG00000185920	23	TSG	Promoter Associated	Island
cg22866426	0.5251715	RUNX1	ENSG00000159216	0	TSG	Promoter Associated	Island
cg17339910	0.399428	RUNX1	ENSG00000159216	0	TSG	Promoter Associated	Island
cg04004558	0.2809271	SOCS1	ENSG00000185338	0	TSG	Promoter Associated	Island
cg27003951	0.2598022	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 Relapse sample. Filtering criteria and integration with RNA-seq is the same as is reported for the Presentation sample (Table 5).

ISSN: 1471-2105