MaGIC: a machine learning tool set and web application for monoallelic gene inference from chromatin

BMC Bioinformatics
Svetlana VinogradovaAlexander A Gimelbrant

Abstract

A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell lineages. MAE is highly cell-type specific and mapping it in a large number of cell and tissue types can provide insight into its biological function. Its detection, however, remains challenging. We previously reported that a sequence-independent chromatin signature identifies, with high sensitivity and specificity, genes subject to MAE in multiple tissue types using readily available ChIP-seq data. Here we present an implementation of this method as a user-friendly, open-source software pipeline for monoallelic gene inference from chromatin (MaGIC). The source code for the MaGIC pipeline and the Shiny app is available at https://github.com/gimelbrantlab/magic . The pipeline can be used by researchers to map monoallelic expression in a variety of cell types using existing models and to train new models with additional sets of chromatin marks.

References

Nov 17, 2007·Science·Alexander GimelbrantAndrew Chess
Jul 20, 2010·Bioinformatics·W J KentD Karolchik
Feb 22, 2012·Genome Biology·Lillian M ZwemerAlexander A Gimelbrant
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Mar 29, 2013·Nature Communications·Euan S PolsonNorman J Maitland
Oct 1, 2013·Current Opinion in Genetics & Development·Virginia SavovaAlexander A Gimelbrant
Jan 2, 2014·ELife·Anwesha NagAlexander A Gimelbrant
Feb 4, 2014·Bioinformatics·Andy Pohl, Miguel Beato
May 2, 2014·Trends in Genetics : TIG·Mélanie A Eckersley-Maslin, David L Spector
Jun 21, 2015·G3 : Genes - Genomes - Genetics·Anwesha NagAlexander A Gimelbrant
Jan 26, 2016·Nature Genetics·Virginia SavovaAlexander A Gimelbrant
Nov 29, 2016·Annual Review of Genetics·Andrew Chess

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Citations

Jun 9, 2021·Nature Communications·Asia MendelevichAlexander A Gimelbrant

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
ChIP-seq
RNA-Seq

Software Mentioned

MaGIC
generate
Docker
R script
analyze
Bwtool
R

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