For each cohort (i.e. colon primary tumors), the samples' methylation distribution is segmented into five bins (tracks) according to their beta values. Namely, beta values below 0.2 indicate the lowest DNA methylation whereas values over 0.8 depict almost full DNA methylation. Color intensity in each track represents the proportion of samples matching the methylation status (the darker, the higher). The stacked five tracks can be thought of as a density plot of the cohort methylation status.
A track depicting differential methylation is available for cohorts with both primary tumors and adjacent normal data. Significant probes show an absolute increment of methylation beta value over 0.2 and under a Wilcoxon test p-value cut-off of 0.001. Gray depicts no detectable differences, red tumor hypermethylations and blue tumor hypomethylations.
The trackhub can be accessed at http://maplab.cat/tcga_450k_trackhub.
If you consider this software useful please cite our paper:
Data have been obtained from the TCGA Research Network. Some datasets have limitations for usage until a global analysis is published; please contact TCGA before publishing.