BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.

2.50
Hdl Handle:
http://hdl.handle.net/10143/85773
Title:
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.
Authors:
Wang, Junbai; Morigen
Citation:
BMC bioinformatics. 2009, 10:345
Additional Links:
http://www.biomedcentral.com/bmcbioinformatics

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Junbaien
dc.contributor.authorMorigenen
dc.date.accessioned2009-11-10T13:04:09Z-
dc.date.available2009-11-10T13:04:09Z-
dc.date.issued2009-
dc.identifier.citationBMC bioinformatics. 2009, 10:345en
dc.identifier.issn1471-2105-
dc.identifier.pmid19857274-
dc.identifier.doi10.1186/1471-2105-10-345-
dc.identifier.urihttp://hdl.handle.net/10143/85773-
dc.description.abstractBACKGROUND: We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential. RESULTS: The method was successfully tested on synthetic ChIP-chip datasets, real yeast ChIP-chip experiments. Subsequently, it was used to estimate condition-specific and species-specific protein-DNA interaction for several yeast TFs. CONCLUSION: The results revealed that the modification of the protein binding parameters and the variation of the individual nucleotide affinity in either recognition or flanking sequences occurred under different stresses and in different species. The findings suggest that such modifications may be adaptive and play roles in the formation of the environment-specific binding patterns of yeast TFs and in the divergence of TF binding sites across the related yeast species.en
dc.language.isoenen
dc.relation.urlhttp://www.biomedcentral.com/bmcbioinformaticsen
dc.subjectVDP::Medisinske Fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk genetikk: 714en
dc.titleBayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.en
dc.typeJournal articleen
dc.typepeer revieweden
dc.contributor.departmentDivision of Pathology, The Norwegian Radium Hospital, Rikshospitalet University Hospital, Montebello 0310 Oslo, Norway. junbai.wang@rr-research.noen
dc.identifier.journalBMC bioinformaticsen
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