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Sequential regulatory activity prediction across chromosomes with convolutional neural networks
Models for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell-type–specific epigenetic and transcriptional profiles in large mammalian genomes from DNA sequ...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932613/ https://www.ncbi.nlm.nih.gov/pubmed/29588361 http://dx.doi.org/10.1101/gr.227819.117 |
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author | Kelley, David R. Reshef, Yakir A. Bileschi, Maxwell Belanger, David McLean, Cory Y. Snoek, Jasper |
author_facet | Kelley, David R. Reshef, Yakir A. Bileschi, Maxwell Belanger, David McLean, Cory Y. Snoek, Jasper |
author_sort | Kelley, David R. |
collection | PubMed |
description | Models for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell-type–specific epigenetic and transcriptional profiles in large mammalian genomes from DNA sequence alone. By use of convolutional neural networks, this system identifies promoters and distal regulatory elements and synthesizes their content to make effective gene expression predictions. We show that model predictions for the influence of genomic variants on gene expression align well to causal variants underlying eQTLs in human populations and can be useful for generating mechanistic hypotheses to enable fine mapping of disease loci. |
format | Online Article Text |
id | pubmed-5932613 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-59326132018-05-31 Sequential regulatory activity prediction across chromosomes with convolutional neural networks Kelley, David R. Reshef, Yakir A. Bileschi, Maxwell Belanger, David McLean, Cory Y. Snoek, Jasper Genome Res Method Models for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell-type–specific epigenetic and transcriptional profiles in large mammalian genomes from DNA sequence alone. By use of convolutional neural networks, this system identifies promoters and distal regulatory elements and synthesizes their content to make effective gene expression predictions. We show that model predictions for the influence of genomic variants on gene expression align well to causal variants underlying eQTLs in human populations and can be useful for generating mechanistic hypotheses to enable fine mapping of disease loci. Cold Spring Harbor Laboratory Press 2018-05 /pmc/articles/PMC5932613/ /pubmed/29588361 http://dx.doi.org/10.1101/gr.227819.117 Text en © 2018 Kelley et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Method Kelley, David R. Reshef, Yakir A. Bileschi, Maxwell Belanger, David McLean, Cory Y. Snoek, Jasper Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title | Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title_full | Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title_fullStr | Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title_full_unstemmed | Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title_short | Sequential regulatory activity prediction across chromosomes with convolutional neural networks |
title_sort | sequential regulatory activity prediction across chromosomes with convolutional neural networks |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5932613/ https://www.ncbi.nlm.nih.gov/pubmed/29588361 http://dx.doi.org/10.1101/gr.227819.117 |
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