Article

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles

2017-06-11

Abstract excerpt

<h4>Motivation</h4> DNA 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 expr...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: c30b99d5-7f95-5d98-95fc-d7e35fed8715
DOI: 10.1101/148726

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profilesDOI 10.1101/148726Read

Integrative Ranking Of Enhancer Networks Facilitates The Discovery Of Epigenetic Markers In CancerSemantic proximity Read

EAGLE: an algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactionsSemantic proximity Read

Improving Infinium MethylationEPIC data processing: focus on enhancers and long noncoding RNA genesSemantic proximity Read

Recapitulation of patient-specific 3D chromatin conformation using machine learning and validation of identified enhancer-gene targetsSemantic proximity Read

Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer.Semantic proximity Read

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation–gene expression associations through across 11 tissues and 4 diseasesSemantic proximity Read

Causal gene regulatory network inference using enhancer activity as a causal anchorSemantic proximity Read

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylationSemantic proximity Read

Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression dataSemantic proximity Read

Leveraging collective regulatory effects of long-range DNA methylations to predict gene expressions and estimate their effects on phenotypes in cancerSemantic proximity Read

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cellsSemantic proximity Read

Subtype-specific enhancer RNAs define transcriptional regulators and prognosis in breast cancersSemantic proximity Read