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Article: PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data

TitlePTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data
Authors
Issue Date2014
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2014, v. 42 n. W1, p. W130-W136 How to Cite?
AbstractInteractions among transcriptional factors (TFs), cofactors and other proteins or enzymes can affect transcriptional regulatory capabilities of eukaryotic organisms. Post-translational modifications (PTMs) cooperate with TFs and epigenetic alterations to constitute a hierarchical complexity in transcriptional gene regulation. While clearly implicated in biological processes, our understanding of these complex regulatory mechanisms is still limited and incomplete. Various online software have been proposed for uncovering transcriptional and epigenetic regulatory networks, however, there is a lack of effective web-based software capable of constructing underlying interactive organizations between post-translational and transcriptional regulatory components. Here, we present an open web server, post-translational hierarchical gene regulatory network (PTHGRN) to unravel relationships among PTMs, TFs, epigenetic modifications and gene expression. PTHGRN utilizes a graphical Gaussian model with partial least squares regression-based methodology, and is able to integrate protein-protein interactions, ChIP-seq and gene expression data and to capture essential regulation features behind high-throughput data. The server provides an integrative platform for users to analyze ready-to-use public high-throughput Omics resources or upload their own data for systems biology study. Users can choose various parameters in the method, build network topologies of interests and dissect their associations with biological functions. Application of the software to stem cell and breast cancer demonstrates that it is an effective tool for understanding regulatory mechanisms in biological complex systems. PTHGRN web server is publically available at web site http://www.byanbioinfo.org/pthgrn.
Persistent Identifierhttp://hdl.handle.net/10722/198459
ISSN
2015 Impact Factor: 9.202
2015 SCImago Journal Rankings: 7.458
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorGuan, Den_US
dc.contributor.authorShao, Jen_US
dc.contributor.authorZhao, Zen_US
dc.contributor.authorWang, Pen_US
dc.contributor.authorQin, Jen_US
dc.contributor.authorDeng, Yen_US
dc.contributor.authorBoheler, KRen_US
dc.contributor.authorWang, JJen_US
dc.contributor.authorYan, Ben_US
dc.date.accessioned2014-07-07T07:00:30Z-
dc.date.available2014-07-07T07:00:30Z-
dc.date.issued2014en_US
dc.identifier.citationNucleic Acids Research, 2014, v. 42 n. W1, p. W130-W136en_US
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10722/198459-
dc.description.abstractInteractions among transcriptional factors (TFs), cofactors and other proteins or enzymes can affect transcriptional regulatory capabilities of eukaryotic organisms. Post-translational modifications (PTMs) cooperate with TFs and epigenetic alterations to constitute a hierarchical complexity in transcriptional gene regulation. While clearly implicated in biological processes, our understanding of these complex regulatory mechanisms is still limited and incomplete. Various online software have been proposed for uncovering transcriptional and epigenetic regulatory networks, however, there is a lack of effective web-based software capable of constructing underlying interactive organizations between post-translational and transcriptional regulatory components. Here, we present an open web server, post-translational hierarchical gene regulatory network (PTHGRN) to unravel relationships among PTMs, TFs, epigenetic modifications and gene expression. PTHGRN utilizes a graphical Gaussian model with partial least squares regression-based methodology, and is able to integrate protein-protein interactions, ChIP-seq and gene expression data and to capture essential regulation features behind high-throughput data. The server provides an integrative platform for users to analyze ready-to-use public high-throughput Omics resources or upload their own data for systems biology study. Users can choose various parameters in the method, build network topologies of interests and dissect their associations with biological functions. Application of the software to stem cell and breast cancer demonstrates that it is an effective tool for understanding regulatory mechanisms in biological complex systems. PTHGRN web server is publically available at web site http://www.byanbioinfo.org/pthgrn.-
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/-
dc.relation.ispartofNucleic Acids Researchen_US
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subject.meshChromatin Immunoprecipitation-
dc.subject.meshGene Expression Profiling-
dc.subject.meshGene Regulatory Networks-
dc.subject.meshProtein Interaction Mapping-
dc.subject.meshSoftware-
dc.titlePTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression dataen_US
dc.typeArticleen_US
dc.identifier.emailQin, J: qinjing@hku.hken_US
dc.identifier.emailBoheler, KR: bohelerk@hku.hken_US
dc.identifier.emailWang, JJ: junwen@hku.hken_US
dc.identifier.authorityBoheler, KR=rp01884en_US
dc.identifier.authorityWang, JJ=rp00280en_US
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/nar/gku471en_US
dc.identifier.pmid24875471-
dc.identifier.hkuros229944en_US
dc.identifier.hkuros243448-
dc.identifier.volume42-
dc.identifier.issueW1-
dc.identifier.spageW130-
dc.identifier.epageW136-
dc.identifier.isiWOS:000339715000023-
dc.publisher.placeUnited Kingdom-

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