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PEDLA: predicting enhancers with a deep learning-based algorithmic framework.

Abstract：

:Transcriptional enhancers are non-coding segments of DNA that play a central role in the spatiotemporal regulation of gene expression programs. However, systematically and precisely predicting enhancers remain a major challenge. Although existing methods have achieved some success in enhancer prediction, they still suffer from many issues. We developed a deep learning-based algorithmic framework named PEDLA (https://github.com/wenjiegroup/PEDLA), which can directly learn an enhancer predictor from massively heterogeneous data and generalize in ways that are mostly consistent across various cell types/tissues. We first trained PEDLA with 1,114-dimensional heterogeneous features in H1 cells, and demonstrated that PEDLA framework integrates diverse heterogeneous features and gives state-of-the-art performance relative to five existing methods for enhancer prediction. We further extended PEDLA to iteratively learn from 22 training cell types/tissues. Our results showed that PEDLA manifested superior performance consistency in both training and independent test sets. On average, PEDLA achieved 95.0% accuracy and a 96.8% geometric mean (GM) of sensitivity and specificity across 22 training cell types/tissues, as well as 95.7% accuracy and a 96.8% GM across 20 independent test cell types/tissues. Together, our work illustrates the power of harnessing state-of-the-art deep learning techniques to consistently identify regulatory elements at a genome-wide scale from massively heterogeneous data across diverse cell types/tissues.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Liu F,Li H,Ren C,Bo X,Shu W

doi

10.1038/srep28517

subject

Has Abstract

pub_date

2016-06-22 00:00:00

pages

28517

issn

2045-2322

pii

srep28517

journal_volume

6

pub_type

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