Predicting Gene Expression from DNA Sequence using Residual Neural Network

Abstract

It is known that cis-acting DNA motifs play an important role in regulating gene expression. The genome in a cell thus contains the information that not only encodes for the synthesis of proteins but also is necessary for regulating expression of genes. Therefore, the mRNA level of a gene may be predictable from the DNA sequence. Indeed, three deep neural network models were developed recently to predict the mRNA level of a gene directly or indirectly from the DNA sequence around the transcription start side of the gene. In this work, we develop a deep residual network model, named ExpResNet, to predict gene expression directly from DNA sequence. Applying ExpResNet to the GTEx data, we demonstrate that ExpResNet outperforms the three existing models across four tissues tested. Our model may be useful in the investigation of gene regulation.