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Table 5 DNA methylation of TSGs in the Presentation sample

From: Enhancing cancer clonality analysis with integrative genomics

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
  1. 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.