bioRxivCancer BiologyPreprint
Cancer methylomes characterization enabled by Rocker-meth
M. Benelli, G. M. Franceschini, A. Magi, D. Romagnoli, C. Biagioni, I. Migliaccio, L. Malorni, A. Di Leo, F. Demichelis
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.
- organism: human
- assay: DNA methylation
- research focus: differential expression
- research focus: gene regulatory network inference
- research focus: chromatin & epigenetic regulation
- approach: deep learning
- approach: statistical model
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Identifying differentially methylated sites in samples with varying tumor purity
Antti Häkkinen, Amjad Alkodsi, … Sampsa Hautaniemi·BioinformaticsPeer-reviewed·Apr 17, 2018
- Machine Classification of Methylomes in Cancer
Izzy Newsham, Marcin Sendera, … Shamith Samarajiwa·Biology Methods and ProtocolsPeer-reviewed·Jan 1, 2024
- DMRIntTk: integrating different DMR sets based on density peak clustering
Wenjin Zhang, Wenlong Jie, … Xiaoqing Peng·bioRxiv·Jul 10, 2024
- Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes
Alexander Titus, Gregory P. Way, … Brock C. Christensen·Scientific ReportsPeer-reviewed·Sep 11, 2017
- coMethDMR: Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
Lissette Gomez, Gabriel Odom, … Lily Wang·Nucleic Acids ResearchPeer-reviewed·Jul 8, 2019
- Locus-specific enrichment analysis of 5-hydroxymethylcytosine reveals novel genes associated with breast carcinogenesis
D. Ramasamy, A. K. D. M. Rao, … S. Mani·bioRxiv·Jun 17, 2022