1 Make sure the file extension you submitted is ‘.txt’ format and the columns are separated by tabs (i.e. a tab-delimited text file should be provided).
2 Intuitively, in your input file, each row contains the methylation levels of one gene across all samples, while each column contains the methylation levels of all genes in one sample. The heading row of your input file indicates the assignment of batch and group for each sample (column). The batch and group assignment of each sample should be connected by '_', e.g. 'batch1_control' or 'batchMay25_siMETTL3'. You may also see the example file by click the EXAMPLE button below. If you have no batch information to be considered, simply assign all samples as 'batch1_'.
3 When the input file is prepared, select the species of your input data and type in your email address then click SUBMIT button to perform the analysis. It usually takes few minutes to perform the correction and comparison analysis. When the job is done, you will receive an email containing the result page URL.
4 After running, you can select one group to see the methylation levels of this groups before and after correction. The corrected methylation profiles can also be downloaded by clicking the DOWNLOAD THE CORRECTED DATA button. Besides, for each gene, a Z-score is also provided by comparing the methylation level of this group and all other methylation profiles in our reference dataset AND the input data. High positive Z-scores indicate hypermethylated genes, while negative Z-scores often suggest hypomethylated genes.
Moreover, the methylation levels of all genes in the group you selected will also be compared with all other methylation profiles in our reference dataset.The methylation profiles showing the top similarities, before and after correction, will be depicted by bar plots.
Finally, you can analyze the enriched function of the hyper- or hypomethylated genes in the selected group by clicking FUNCTIONAL ENRICHMENT ANALYSIS button. The functional enrichment analysis will be performed in a new window. After select the function annotation set category and the threshold for choosing hyper- (or hypo-) methylated genes, click the PLOT button, and then the top enriched functions will be illustrated. The functional enrichment analysis results can also be downloaded by clicking the DOWNLOAD RESULTS button.