Table 2 Feature comparison of MethGET with other tools
MethGET | COHCAP | PiiL | ViewBS | MethHC | iMETHYL | |
|---|---|---|---|---|---|---|
Inputs with methylation and expression data | â—‹ | â—‹ | â—‹ | X (Using gene region files with different expression values) | No input | No input |
Customized analyses | â—‹ | â—‹ | â—‹ | â—‹ | X | X |
Web interface | â—‹ | X | X | X | â—‹ | â—‹ |
Multiple-methylome analyses | â—‹ | â—‹ | â—‹ | â—‹ | â—‹ | X |
Supported species | Any species with annotated genome | Species with CpG island annotation | Species with pathway annotation | Species with region file | Homo sapiens | Homo sapiens |
Sequence context of cytosine methylation | CG, CHG, CHH | CG | CG | CG, CHG, CHH | CG | CG |
Target regions | Genome-wide | Selected CpG islands | Genes in the pathway | Genome-wide | Selected genes | Selected genes or regions |
Genomic locations | Gene body, promoter, exon, intron, TE | CpG islands | Annotated CpG sites | Regions in region files | 8 Gene regions+, 5 CpG Island regions | Only selected cytosines |
Correlation analyses | 6 analyses | 1 (Scatterplot) | Visualization | 1 (Metagene plot) | 1 (Scatterplot) | Visualization |
Citation | Teng et al. (2020) | Warden et al. (2013) [21] | Moghadam et al. (2017) [22] | Huang et al. (2018) [23] | Huang et al. (2015) [24] | Komaki et al. (2018) [25] |