Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Kelley, David R., Reshef, Yakir A., Bileschi, Maxwell, Belanger, David, McLean, Cory Y., Snoek, Jasper
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
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
Descripción
Sumario: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.