WordCluster: detecting clusters of DNA words and genomic elements
Identifieur interne : 001340 ( Pmc/Checkpoint ); précédent : 001339; suivant : 001341WordCluster: detecting clusters of DNA words and genomic elements
Auteurs : Michael Hackenberg [Espagne] ; Pedro Carpena [Espagne, États-Unis] ; Pedro Bernaola-Galván [Espagne] ; Guillermo Barturen [Espagne] ; Ángel M. Alganza [Espagne] ; José L. Oliver [Espagne]Source :
- Algorithms for Molecular Biology : AMB [ 1748-7188 ] ; 2011.
Abstract
Many
We introduce here an algorithm to detect clusters of DNA words (
Url:
DOI: 10.1186/1748-7188-6-2
PubMed: 21261981
PubMed Central: 3037320
Affiliations:
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PMC:3037320Le document en format XML
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Alganza</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. 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18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><affiliation wicri:level="2"><nlm:aff id="I2">Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física 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xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region></placeName></affiliation></author><author><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Ángel M" last="Alganza">Ángel M. Alganza</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author><author><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name><affiliation wicri:level="4"><nlm:aff id="I1">Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada</wicri:regionArea><placeName><region nuts="2" type="communauté">Andalousie</region><settlement type="city">Grenade (Espagne)</settlement></placeName><orgName type="university">Université de Grenade</orgName></affiliation></author></analytic><series><title level="j">Algorithms for Molecular Biology : AMB</title><idno type="eISSN">1748-7188</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Many <italic>k-</italic>mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</p></sec><sec><title>Results</title><p>We introduce here an algorithm to detect clusters of DNA words (<italic>k-</italic>mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used <italic>WordCluster </italic>to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</p></sec><sec><title>Conclusions</title><p><italic>WordCluster </italic>seems to predict biological meaningful clusters of DNA words (<italic>k-</italic>mers) and genomic entities. The implementation of the method into a web server is available at <ext-link ext-link-type="uri" xlink:href="http://bioinfo2.ugr.es/wordCluster/wordCluster.php">http://bioinfo2.ugr.es/wordCluster/wordCluster.php</ext-link> including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Durand, D" uniqKey="Durand D">D Durand</name></author><author><name sortKey="Sankoff, D" uniqKey="Sankoff D">D Sankoff</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gardiner Garden, M" uniqKey="Gardiner Garden M">M Gardiner-Garden</name></author><author><name sortKey="Frommer, M" uniqKey="Frommer M">M Frommer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Makeev, Vj" uniqKey="Makeev V">VJ Makeev</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Algorithms Mol Biol</journal-id><journal-title-group><journal-title>Algorithms for Molecular Biology : AMB</journal-title></journal-title-group><issn pub-type="epub">1748-7188</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21261981</article-id><article-id pub-id-type="pmc">3037320</article-id><article-id pub-id-type="publisher-id">1748-7188-6-2</article-id><article-id pub-id-type="doi">10.1186/1748-7188-6-2</article-id><article-categories><subj-group subj-group-type="heading"><subject>Software Article</subject></subj-group></article-categories><title-group><article-title><italic>WordCluster</italic>: detecting clusters of DNA words and genomic elements</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Hackenberg</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>mlhack@gmail.com</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Carpena</surname><given-names>Pedro</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>pcarpena@ctima.uma.es</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Bernaola-Galván</surname><given-names>Pedro</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>rick@uma.es</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Barturen</surname><given-names>Guillermo</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>bartg01@gmail.com</email></contrib><contrib contrib-type="author" id="A5"><name><surname>Alganza</surname><given-names>Ángel M</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>ama@ugr.es</email></contrib><contrib contrib-type="author" corresp="yes" id="A6"><name><surname>Oliver</surname><given-names>José L</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>oliver@ugr.es</email></contrib></contrib-group><aff id="I1"><label>1</label>Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada & Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100-Granada, Spain</aff><aff id="I2"><label>2</label>Dpto. de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga 29071-Malaga, Spain</aff><aff id="I3"><label>3</label>Division of Sleep Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, MA 02115, USA</aff><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>24</day><month>1</month><year>2011</year></pub-date><volume>6</volume><fpage>2</fpage><lpage>2</lpage><history><date date-type="received"><day>30</day><month>8</month><year>2010</year></date><date date-type="accepted"><day>24</day><month>1</month><year>2011</year></date></history><permissions><copyright-statement>Copyright ©2011 Hackenberg et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>Hackenberg et al; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.almob.org/content/6/1/2"></self-uri><abstract><sec><title>Background</title><p>Many <italic>k-</italic>mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds.</p></sec><sec><title>Results</title><p>We introduce here an algorithm to detect clusters of DNA words (<italic>k-</italic>mers), or any other genomic element, based on the distance between consecutive copies and an assigned statistical significance. We implemented the method into a web server connected to a MySQL backend, which also determines the co-localization with gene annotations. We demonstrate the usefulness of this approach by detecting the clusters of CAG/CTG (cytosine contexts that can be methylated in undifferentiated cells), showing that the degree of methylation vary drastically between inside and outside of the clusters. As another example, we used <italic>WordCluster </italic>to search for statistically significant clusters of olfactory receptor (OR) genes in the human genome.</p></sec><sec><title>Conclusions</title><p><italic>WordCluster </italic>seems to predict biological meaningful clusters of DNA words (<italic>k-</italic>mers) and genomic entities. The implementation of the method into a web server is available at <ext-link ext-link-type="uri" xlink:href="http://bioinfo2.ugr.es/wordCluster/wordCluster.php">http://bioinfo2.ugr.es/wordCluster/wordCluster.php</ext-link> including additional features like the detection of co-localization with gene regions or the annotation enrichment tool for functional analysis of overlapped genes.</p></sec></abstract></article-meta></front></pmc><affiliations><list><country><li>Espagne</li><li>États-Unis</li></country><region><li>Andalousie</li><li>Massachusetts</li></region><settlement><li>Grenade (Espagne)</li></settlement><orgName><li>Université de Grenade</li></orgName></list><tree><country name="Espagne"><region name="Andalousie"><name sortKey="Hackenberg, Michael" sort="Hackenberg, Michael" uniqKey="Hackenberg M" first="Michael" last="Hackenberg">Michael Hackenberg</name></region><name sortKey="Alganza, Angel M" sort="Alganza, Angel M" uniqKey="Alganza A" first="Ángel M" last="Alganza">Ángel M. Alganza</name><name sortKey="Barturen, Guillermo" sort="Barturen, Guillermo" uniqKey="Barturen G" first="Guillermo" last="Barturen">Guillermo Barturen</name><name sortKey="Bernaola Galvan, Pedro" sort="Bernaola Galvan, Pedro" uniqKey="Bernaola Galvan P" first="Pedro" last="Bernaola-Galván">Pedro Bernaola-Galván</name><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name><name sortKey="Oliver, Jose L" sort="Oliver, Jose L" uniqKey="Oliver J" first="José L" last="Oliver">José L. Oliver</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Carpena, Pedro" sort="Carpena, Pedro" uniqKey="Carpena P" first="Pedro" last="Carpena">Pedro Carpena</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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