Introduction

Recently, many studies suggest that enhancers play a major role as regulators of cell-specific phenotypes leading to alteration in transcriptomes realated to diseases . In order to investigate regulatory enhancers that can be located at long distances upstream or downstream of target genes Bioconductor offer the Enhancer Linking by Methylation/Expression Relationship (ELMER) package. This package is designed to combine DNA methylation and gene expression data from human tissues to infer multi-level cis-regulatory networks. It uses DNA methylation to identify enhancers and correlates their state with expression of nearby genes to identify one or more transcriptional targets. Transcription factor (TF) binding site analysis of enhancers is coupled with expression analysis of all TFs to infer upstream regulators.

Input

ELMER's input is a specific R object called MAE (MultiAssay Experiment) which contains a matrix of DNA methylation and a matrix of gene expression, a table with Sample information and a table mapping sample to DNA methylation and to gene expression.

ELMER steps

Step 1 | Identify distal probes on HM450K.
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Step 2 | Identify distal probes with significantly different DNA methyaltion level in Group1 and VS Group2.
Step 3 | Identify putative target genes for differentially methylated distal probes.
Step 4 | Identify enriched motifs for the distal probes which are significantly differentially methylated and linked to putative target gene.
Step 5 | Identify regulatory TFs whose expression associate with DNA methylation at motifs.