Figure 1

Data input and usage flowchart. Methylation plotter uses beta-values as input. These can be obtained directly from methylation array platforms such as the Illumina Infinium 450k, downloaded from databases like the TCGA or from bisulfite-treated DNA sequencing. For instance, direct bisulfite sequencing provides an estimation of the beta-value of each cytosine. In this case, the C to T peak height ratio can be assessed by naked eye and reflects the methylation status of that position. Once obtained the beta values, the user may use a spreadsheet editor (Microsoft Excel, LibreOffice Calc) to format the data and to export it to a tab-separated text file. Finally, the upload of this file to the webpage will produce the methylation plot and the rest of graphical and statistical outputs. The plotting options (data sorting, plot type, image width and height) are dynamically changed without the need of reuploading the data.