RESET is a computational methodology to identify aberrant DNA methylation and associated cis-transcriptional changes across tumors.
More specifically, RESET analyzes large-scale DNA methylation sample cohorts to test for the presence of aberrant DNA methylation at gene TSS and assess whether aberrant methylation states lead to epigenetic silencing or enhancing of gene expression.
We applied RESET to 23 cancer cohorts (6,010 human samples) molecularly profiled by The Cancer Genome Atlas (TCGA) with available DNA methylomes generated by the Illumina Infinium HM450 array.
In total, we identified 64,414 probes - mapping to 12,053 genes - that have low DNA methylation across all normal samples, and 3,423 probes - mapping to 2,006 genes - that have high DNA methylation across all normal samples. Ouf of these, we found 581 epigenetically silenced and 85 epigenetically enhanced genes.
If you use this tool or data, please cite the following publication:
Saghafinia S., Mina M., Riggi N., Hanahan D. and Ciriello G. (2018) Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Reports (In Press)
The R implementation of RESET.