PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

Abstract Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate me...

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Autores principales:	Ming-Ju Tsai, Jyun-Rong Wang, Chi-Dung Yang, Kuo-Ching Kao, Wen-Lin Huang, Hsi-Yuan Huang, Ching-Ping Tseng, Hsien-Da Huang, Shinn-Ying Ho
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/19d67019f9d741479c60060d8c2fd16f
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spelling	oai:doaj.org-article:19d67019f9d741479c60060d8c2fd16f2021-12-02T15:08:25ZPredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli10.1038/s41598-017-18648-52045-2322https://doaj.org/article/19d67019f9d741479c60060d8c2fd16f2018-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-18648-5https://doaj.org/toc/2045-2322Abstract Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate method PredCRP to derive an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites. A dataset consisting of 169 CRP-binding sites with regulatory roles strongly supported by evidence was compiled. The PredCRP-model, using 12 informative features of CRP-binding sites, and cooperating with a support vector machine achieved a training and test accuracy of 0.98 and 0.93, respectively. PredCRP-ruleset has two activation rules and two repression rules derived using the 12 features and the decision tree method C4.5. This work further screened and identified 23 previously unobserved regulatory interactions in Escherichia coli. Using quantitative PCR for validation, PredCRP-model and PredCRP-ruleset achieved a test accuracy of 0.96 (=22/23) and 0.91 (=21/23), respectively. The proposed method is suitable for designing predictors for regulatory roles of all global regulators in Escherichia coli. PredCRP can be accessed at https://github.com/NctuICLab/PredCRP .Ming-Ju TsaiJyun-Rong WangChi-Dung YangKuo-Ching KaoWen-Lin HuangHsi-Yuan HuangChing-Ping TsengHsien-Da HuangShinn-Ying HoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-9 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ming-Ju Tsai Jyun-Rong Wang Chi-Dung Yang Kuo-Ching Kao Wen-Lin Huang Hsi-Yuan Huang Ching-Ping Tseng Hsien-Da Huang Shinn-Ying Ho PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
description	Abstract Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate method PredCRP to derive an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites. A dataset consisting of 169 CRP-binding sites with regulatory roles strongly supported by evidence was compiled. The PredCRP-model, using 12 informative features of CRP-binding sites, and cooperating with a support vector machine achieved a training and test accuracy of 0.98 and 0.93, respectively. PredCRP-ruleset has two activation rules and two repression rules derived using the 12 features and the decision tree method C4.5. This work further screened and identified 23 previously unobserved regulatory interactions in Escherichia coli. Using quantitative PCR for validation, PredCRP-model and PredCRP-ruleset achieved a test accuracy of 0.96 (=22/23) and 0.91 (=21/23), respectively. The proposed method is suitable for designing predictors for regulatory roles of all global regulators in Escherichia coli. PredCRP can be accessed at https://github.com/NctuICLab/PredCRP .
format	article
author	Ming-Ju Tsai Jyun-Rong Wang Chi-Dung Yang Kuo-Ching Kao Wen-Lin Huang Hsi-Yuan Huang Ching-Ping Tseng Hsien-Da Huang Shinn-Ying Ho
author_facet	Ming-Ju Tsai Jyun-Rong Wang Chi-Dung Yang Kuo-Ching Kao Wen-Lin Huang Hsi-Yuan Huang Ching-Ping Tseng Hsien-Da Huang Shinn-Ying Ho
author_sort	Ming-Ju Tsai
title	PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
title_short	PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
title_full	PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
title_fullStr	PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
title_full_unstemmed	PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli
title_sort	predcrp: predicting and analysing the regulatory roles of crp from its binding sites in escherichia coli
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/19d67019f9d741479c60060d8c2fd16f
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PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli

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