Genome Functional Annotation using Deep Convolutional Neural Network

Abstract

Deep neural network application is today a skyrocketing field in many disciplinary domains. In genomics the development of deep neural networks is expected to revolutionize current practice. Several approaches relying on convolutional neural networks have been developed to associate short genomic sequences with a functional role such as promoters, enhancers or protein binding sites along genomes. These approaches rely on the generation of sequences batches with known annotations for learning purpose. While they show good performance to predict annotations from a test subset of these batches, they usually perform poorly when applied genome-wide.\n\nIn this study, we address this issue and propose an optimal strategy to train convolutional neural networks for this specific application. We use as a case study transcription start sites and show that a model trained on one organism can be used to predict transcription start sites in a different specie. This cross-species application of convolutional neural networks trained with genomic sequence data provides a new technique to annotate any genome from previously existing annotations in related species. It also provides a way to determine whether the sequence patterns recognized by chromatin associated proteins in different species are conserved or not.