Mehwish Gill, Muhammad Kabir, Saeed Ahmed, Muhammad Asif Subhani, Maqsood Hayat
{"title":"A Comparative Review and Analysis of Computational Predictors for\u0000Identification of Enhancer and their Strength","authors":"Mehwish Gill, Muhammad Kabir, Saeed Ahmed, Muhammad Asif Subhani, Maqsood Hayat","doi":"10.2174/0115748936285942240513064919","DOIUrl":"https://doi.org/10.2174/0115748936285942240513064919","url":null,"abstract":"\u0000\u0000Enhancers are the short functional regions (50–1500bp) in the genome, which play an\u0000effective character in activating gene-transcription in the presence of transcription-factors (TFs).\u0000Many human diseases, such as cancer and inflammatory bowel disease, are correlated with the enhancers’\u0000genetic variations. The precise recognition of the enhancers provides useful insights for\u0000understanding the pathogenesis of human diseases and their treatments. High-throughput experiments\u0000are considered essential tools for characterizing enhancers; however, these methods are laborious,\u0000costly and time-consuming. Computational methods are considered alternative solutions for\u0000accurate and rapid identification of the enhancers. Over the past years, numerous computational\u0000predictors have been devised for predicting enhancers and their strength. A comprehensive review\u0000and thorough assessment are indispensable to systematically compare sequence-based enhancer’s\u0000bioinformatics tools on their performance. Giving the increasing interest in this domain, we conducted\u0000a large-scale analysis and assessment of the state-of-the-art enhancer predictors to evaluate\u0000their scalability and generalization power. Additionally, we classified the existing approaches into\u0000three main groups: conventional machine-learning, ensemble and deep learning-based approaches.\u0000Furthermore, the study has focused on exploring the important factors that are crucial for developing\u0000precise and reliable predictors such as designing trusted benchmark/independent datasets, feature\u0000representation schemes, feature selection methods, classification strategies, evaluation metrics\u0000and webservers. Finally, the insights from this review are expected to provide important guidelines\u0000to the research community and pharmaceutical companies in general and high-throughput tools for\u0000the detection and characterization of enhancers in particular.\u0000","PeriodicalId":10801,"journal":{"name":"Current Bioinformatics","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141387227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}