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Article: An integrative method to decode regulatory logics in gene transcription

TitleAn integrative method to decode regulatory logics in gene transcription
Authors
Issue Date2017
PublisherNature Publishing Group: Nature Communications. The Journal's web site is located at http://www.nature.com/ncomms/index.html
Citation
Nature Communications, 2017, v. 8, article no. 1044, p. 1-12 How to Cite?
AbstractModeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple TFs, is still challenging. In this study, we introduced an integrative method, LogicTRN, to decode TF-TF interactions that form TF logics in regulating target genes. By combining cis-regulatory logics and transcriptional kinetics into one single model framework, LogicTRN can naturally integrate dynamic gene expression data and TF-DNA binding signals in order to identify the TF logics and to reconstruct the underlying TRNs. We evaluated the newly developed methodology using simulation, comparison and application studies, and the results not only show their consistence with existing knowledge, but also demonstrate its ability to accurately reconstruct TRNs in biological complex systems.
Persistent Identifierhttp://hdl.handle.net/10722/243746
ISSN
2017 Impact Factor: 12.353
2015 SCImago Journal Rankings: 6.539
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYan, B-
dc.contributor.authorGuan, D-
dc.contributor.authorWang, C-
dc.contributor.authorWang, JJ-
dc.contributor.authorHe, B-
dc.contributor.authorQin, J-
dc.contributor.authorBoheler, KR-
dc.contributor.authorLu, A-
dc.contributor.authorZhang, G-
dc.contributor.authorZhu, H-
dc.date.accessioned2017-08-25T02:58:58Z-
dc.date.available2017-08-25T02:58:58Z-
dc.date.issued2017-
dc.identifier.citationNature Communications, 2017, v. 8, article no. 1044, p. 1-12-
dc.identifier.issn2041-1723-
dc.identifier.urihttp://hdl.handle.net/10722/243746-
dc.description.abstractModeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple TFs, is still challenging. In this study, we introduced an integrative method, LogicTRN, to decode TF-TF interactions that form TF logics in regulating target genes. By combining cis-regulatory logics and transcriptional kinetics into one single model framework, LogicTRN can naturally integrate dynamic gene expression data and TF-DNA binding signals in order to identify the TF logics and to reconstruct the underlying TRNs. We evaluated the newly developed methodology using simulation, comparison and application studies, and the results not only show their consistence with existing knowledge, but also demonstrate its ability to accurately reconstruct TRNs in biological complex systems.-
dc.languageeng-
dc.publisherNature Publishing Group: Nature Communications. The Journal's web site is located at http://www.nature.com/ncomms/index.html-
dc.relation.ispartofNature Communications-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleAn integrative method to decode regulatory logics in gene transcription-
dc.typeArticle-
dc.identifier.emailYan, B: yanbin14@hku.hk-
dc.identifier.emailBoheler, KR: bohelerk@hku.hk-
dc.identifier.authorityYan, B=rp01940-
dc.identifier.authorityWang, JJ=rp00280-
dc.identifier.authorityBoheler, KR=rp01884-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1038/s41467-017-01193-0-
dc.identifier.pmid29051499-
dc.identifier.scopuseid_2-s2.0-85031918428-
dc.identifier.hkuros275271-
dc.identifier.hkuros290442-
dc.identifier.volume8-
dc.identifier.spage1044:1-
dc.identifier.epage1044:12-
dc.identifier.isiWOS:000413197100004-
dc.publisher.placeUnited Kingdom-

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