Table 9 Comparing three co-methylation studies
From: Thorough statistical analyses of breast cancer co-methylation patterns
| Â | 2013 study by Akulenko and Helms | 2020 study by Mallona et al. | Our study |
|---|---|---|---|
Tissue/Cancer | Breast cancer | Colon cancer | Breast cancer |
Data type | Illumina 27K (27500) | Illumina 450K (485577) | Illumina 450K (485577) |
CGs or genes used | 13,133 genes | ~  300,000 CG sites | 272,990 CG sites |
Analysis unit | Gene | CG (or probe) | CG (or probe) |
Sample size | 317 tumor and 27 adjacent normal | (1) 90 tumor and 90 adjacent normal (2) 256 tumor and 38 adjacent normal | 53 tumor and 53 adjacent normal |
Tumor vs. normal | Combined | Separated & compared | Separated & compared |
Relationship with genomic distance | Yes | Yes | Yes |
Gene or CG pairs on the same chromosome | 74/187 gene pairs | No specific result | 45.2 million CG pairs for normal; 17.5 million CG pairs for tumor |
Negative correlation | No | Yes | Yes |
Number of high correlation partners | No | Yes | Yes |
ChrX co-methylation | No | No | Yes |
Highly changing sites | No | No | Yes |
Relationship with DM sites | No | No | Yes |