Dataset Information

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

ABSTRACT: BACKGROUND: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. RESULTS: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 . CONCLUSION: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.

SUBMITTER: Vinogradova S

PROVIDER: S-EPMC6394031 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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

Vinogradova Svetlana S Saksena Sachit D SD Ward Henry N HN Vigneau Sébastien S Gimelbrant Alexander A AA

BMC bioinformatics 20190228 1

<h4>Background</h4>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.<h4>Results</h4>We previously reported that a sequence-independent chromatin ...[more]

PMID: 30819107

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Dataset Information

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

Publications

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

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