{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T05:20:08Z","timestamp":1674710408012},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Modern experimental methods provide substantial information on protein\u2013DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code.<\/jats:p>\n               <jats:p>Results: We constructed binding motifs for TFs forming a complex with HIF-1\u03b1 at the erythropoietin 3\u2032-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.<\/jats:p>\n               <jats:p>Contact: \u00a0ivan.kulakovskiy@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr453","type":"journal-article","created":{"date-parts":[[2011,8,19]],"date-time":"2011-08-19T00:51:34Z","timestamp":1313715094000},"page":"2621-2624","source":"Crossref","is-referenced-by-count":5,"title":["A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites"],"prefix":"10.1093","volume":"27","author":[{"given":"I. V.","family":"Kulakovskiy","sequence":"first","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"},{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"A. A.","family":"Belostotsky","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"A. S.","family":"Kasianov","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"N. G.","family":"Esipova","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"Y. A.","family":"Medvedeva","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"},{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"I. A.","family":"Eliseeva","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]},{"given":"V. J.","family":"Makeev","sequence":"additional","affiliation":[{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"},{"name":"1 Laboratory of Bioinformatics and System Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, 2Laboratory of Bioinformatics, Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow 117545, 3Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991 and 4Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia"}]}],"member":"286","published-online":{"date-parts":[[2011,8,18]]},"reference":[{"key":"2023012512002908800_B1","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/btk032","article-title":"Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression","volume":"22","author":"Boeva","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512002908800_B2","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1748-7188-2-13","article-title":"Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules","volume":"2","author":"Boeva","year":"2007","journal-title":"Algorithms Mol. 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