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bioRxiv · 10.1101/148726

Enhancer Linking by Methylation/Expression Relationships with the R package ELMER version 2

Chedraoui Silva, T.·Coetzee, S. G.·Yao, L.·Hazelett, D. J.·Noushmehr, H.·Berman, B. P.
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Abstract

MotivationDNA methylation has been used to identify functional changes at transcriptional enhancers and other cis-regulatory modules (CRMs) in tumors and other disease tissues. Our R/Bioconductor package ELMER (Enhancer Linking by Methylation/Expression Relationships) provides a systematic approach that reconstructs altered gene regulatory networks (GRNs) by combining enhancer methylation and gene expression data derived from the same sample set.\n\nResultsWe present a completely revised version 2 of ELMER that provides numerous new features including an optional web-based interface and a new Supervised Analysis mode to use pre-defined sample groupings. We show that this approach can identify GRNs associated with many new Master Regulators including KLF5 in breast cancer.\n\nAvailabilityELMER v.2 is available as an R/Bioconductor package at http://bioconductor.org/packages/ELMER/

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Chedraoui Silva, T., Coetzee, S. G., Yao, L., Hazelett, D. J., Noushmehr, H., Berman, B. P.. 2017-06-11. Enhancer Linking by Methylation/Expression Relationships with the R package ELMER version 2. https://doi.org/10.1101/148726

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