File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: A mammalian promoter model links cis elements to genetic networks

TitleA mammalian promoter model links cis elements to genetic networks
Authors
Issue Date2006
PublisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/wps/find/journaldescription.cws_home/622790/description
Citation
Biochemical And Biophysical Research Communications, 2006, v. 347 n. 1, p. 166-177 How to Cite?
AbstractAn accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at http://cagr.pcbi.upenn.edu/PSPA. © 2006 Elsevier Inc. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/147538
ISSN
2015 Impact Factor: 2.371
2015 SCImago Journal Rankings: 1.152
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Jen_US
dc.contributor.authorHannenhalli, Sen_US
dc.date.accessioned2012-05-29T06:04:27Z-
dc.date.available2012-05-29T06:04:27Z-
dc.date.issued2006en_US
dc.identifier.citationBiochemical And Biophysical Research Communications, 2006, v. 347 n. 1, p. 166-177en_US
dc.identifier.issn0006-291Xen_US
dc.identifier.urihttp://hdl.handle.net/10722/147538-
dc.description.abstractAn accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at http://cagr.pcbi.upenn.edu/PSPA. © 2006 Elsevier Inc. All rights reserved.en_US
dc.languageengen_US
dc.publisherAcademic Press. The Journal's web site is located at http://www.elsevier.com/wps/find/journaldescription.cws_home/622790/descriptionen_US
dc.relation.ispartofBiochemical and Biophysical Research Communicationsen_US
dc.subject.meshAnimalsen_US
dc.subject.meshBinding Sitesen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshCpg Islands - Geneticsen_US
dc.subject.meshHumansen_US
dc.subject.meshMammalsen_US
dc.subject.meshModels, Geneticen_US
dc.subject.meshPromoter Regions, Genetic - Geneticsen_US
dc.subject.meshProtein Bindingen_US
dc.subject.meshRegulatory Elements, Transcriptional - Geneticsen_US
dc.subject.meshSequence Analysis, Dna - Methodsen_US
dc.subject.meshSignal Transduction - Geneticsen_US
dc.subject.meshTranscription Factors - Geneticsen_US
dc.subject.meshTranscription, Genetic - Geneticsen_US
dc.titleA mammalian promoter model links cis elements to genetic networksen_US
dc.typeArticleen_US
dc.identifier.emailWang, J:junwen@hkucc.hku.hken_US
dc.identifier.authorityWang, J=rp00280en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1016/j.bbrc.2006.06.062en_US
dc.identifier.pmid16806065-
dc.identifier.scopuseid_2-s2.0-33745744510en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-33745744510&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume347en_US
dc.identifier.issue1en_US
dc.identifier.spage166en_US
dc.identifier.epage177en_US
dc.identifier.isiWOS:000239198000023-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridWang, J=8950599500en_US
dc.identifier.scopusauthoridHannenhalli, S=6603889650en_US

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats