The identification of cis-regulatory elements: a review from a machine learning perspective

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Journal titleBiosystems
Subjectcis-regulatory elements; gene regulation; enhancers; promoters; machine learning; deep learning; ensemble learning; data integration
AbstractThe majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These regulatory elements can play crucial roles in controlling gene expressions in specific cell types, conditions, and developmental stages. Disruption to these regions could contribute to phenotype changes. Precisely identifying regulatory elements is key to deciphering the mechanisms underlying transcriptional regulation. Cis-regulatory events are complex processes that involve chromatin accessibility, transcription factor binding, DNA methylation, histone modifications, and the interactions between them. The development of next-generation sequencing techniques has allowed us to capture these genomic features in depth. Applied analysis of genome sequences for clinical genetics has increased the urgency for detecting these regions. However, the complexity of cis-regulatory events and the deluge of sequencing data require accurate and efficient computational approaches, in particular, machine learning techniques. In this review, we describe machine learning approaches for predicting transcription factor binding sites, enhancers, and promoters, primarily driven by next-generation sequencing data. Data sources are provided in order to facilitate testing of novel methods. The purpose of this review is to attract computational experts and data scientists to advance this field.
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AffiliationInformation and Communication Technologies; National Research Council Canada
Peer reviewedYes
NPARC number23001686
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Record identifierea1c02bf-72b9-41fe-9899-9bb12bc3d681
Record created2017-03-17
Record modified2017-03-17
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