Show simple item record

dc.contributor.authorKulakovskiy, Ivan V.
dc.contributor.authorBelostotsky, A. A.
dc.contributor.authorKasianov, Artem S.
dc.contributor.authorEsipova, Natalia G.
dc.contributor.authorMedvedeva, Yulia
dc.contributor.authorEliseeva, Irina A.
dc.contributor.authorMakeev, Vsevolod J.
dc.date.accessioned2015-08-03T09:32:15Z
dc.date.available2015-08-03T09:32:15Z
dc.date.issued2011-08-18
dc.identifier.citationKulakovskiy, I. V., Belostotsky, A. A., Kasianov, A. S., Esipova, N. G., Medvedeva, Y. A., Eliseeva, I. A., & Makeev, V. J. (2011). A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites. Bioinformatics, 27(19), 2621–2624. doi:10.1093/bioinformatics/btr453
dc.identifier.issn13674803
dc.identifier.pmid21852305
dc.identifier.doi10.1093/bioinformatics/btr453
dc.identifier.urihttp://hdl.handle.net/10754/561843
dc.description.abstractMotivation: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. Results: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3'-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. © The Author 2011. Published by Oxford University Press. All rights reserved.
dc.publisherOxford University Press (OUP)
dc.titleA deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.identifier.journalBioinformatics
dc.contributor.institutionLaboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
dc.contributor.institutionLaboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, Russian Federation
dc.contributor.institutionLaboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russian Federation
dc.contributor.institutionGroup of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
kaust.personMedvedeva, Yulia
dc.date.published-online2011-08-18
dc.date.published-print2011-10-01


This item appears in the following Collection(s)

Show simple item record