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bioRxiv · 10.1101/2020.10.09.332759

Cancer methylomes characterization enabled by Rocker-meth

Benelli, M.·Franceschini, G. M.·Magi, A.·Romagnoli, D.·Biagioni, C.·Migliaccio, I.·Malorni, L.·Di Leo, A.·Demichelis, F.
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Abstract

Differentially DNA methylated regions (DMRs) inform on the role of epigenetic changes in cancer. We present Rocker-meth, a computational method exploiting a heterogeneous hidden Markov model to detect DMRs across multiple experimental platforms. Its application to more than 6,000 methylation profiles across 14 tumor types provides a comprehensive catalog of tumor type-specific and shared DMRs, also amenable to single-cell DNA-methylation data. In depth integrative analysis including orthogonal omics shows the enhanced ability of Rocker-meth in recapitulating known associations, further uncovering the pan-cancer relationship between DNA hypermethylation and transcription factor deregulation depending on the baseline chromatin state.

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Benelli, M., Franceschini, G. M., Magi, A., Romagnoli, D., Biagioni, C., Migliaccio, I., Malorni, L., Di Leo, A., Demichelis, F.. 2020-10-09. Cancer methylomes characterization enabled by Rocker-meth. https://doi.org/10.1101/2020.10.09.332759

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