EnhancerTracker: Comparing cell-type-specific enhancer activity of DNA sequence triplets via an ensemble of deep convolutional neural networks

Abstract

MotivationTranscriptional enhancers -- unlike promoters -- are unrestrained by distance or strand orientation with respect to their target genes, making their computational identification a challenge. Further, there are insufficient numbers of confirmed enhancers for many cell types, preventing robust training of machine-learning-based models for enhancer prediction for such cell types. ResultsWe present EnhancerTracker, a novel tool that leverages an ensemble of deep separable convolutional neural networks to identify cell-type-specific enhancers with the need of only two confirmed enhancers. EnhancerTracker is trained, validated, and tested on 52,789 putative enhancers obtained from the FANTOM5 Project and control sequences derived from the human genome. Unlike available tools, which accept one sequence at a time, the input to our tool is three sequences; the first two are enhancers active in the same cell type. EnhancerTracker outputs 1 if the third sequence is an enhancer active in the same cell type(s) where the first two enhancers are active. It outputs 0 otherwise. On a held-out set (15%), EnhancerTracker achieved an accuracy of 64%, a specificity of 93%, a recall of 35%, a precision of 84%, and an F1 score of 49%. Availability and implementationhttps://github.com/BioinformaticsToolsmith/EnhancerTracker Contacthani.girgis@tamuk.edu