DeepEpi: Deep Learning Model for Predicting Gene Expression Regulation Based on Epigenetic Histone Modifications

Abstract

Background: Histone modification is a vital element in gene expression regulation. The way in which these proteins bind to the DNA impacts whether or not a gene may be expressed. Although those factors cannot influence DNA construction, they can influence how it is transcribed. Objective: Each spatial location in DNA has its function, so the spatial arrangement of chromatin modifications affects how the gene can express. Also, gene regulation is affected by the type of histone modification combinations that are present on the gene and depends on the spatial distributional pattern of these modifications and how long these modifications read on a gene region. So, this study aims to know how to model Long-range spatial genome data and model complex dependencies among Histone reads. Methods: The Convolution Neural Network (CNN) is used to model all data features in this paper. It can detect patterns in histones signals and preserve the spatial information of these patterns. It also uses the concept of memory in long short-term memory (LSTM), using vanilla LSTM, Bi-Directional LSTM, or Stacked LSTM to preserve long-range histones signals. Additionally, it tries to combine these methods using ConvLSTM or uses them together with the aid of a self-attention. Results: Based on the results, the combination of CNN, LSTM with the self-attention mechanism obtained an Area under the Curve (AUC) score of 88.87% over 56 cell types. Conclusion: The result outperforms the present state-of-the-art model and provides insight into how combinatorial interactions between histone modification marks can control gene expression. The source code is available at https://github.com/RaniaHamdy/DeepEpi.