DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Identifieur interne : 000367 ( Pmc/Curation ); précédent : 000366; suivant : 000368DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Auteurs : Jérôme Audoux [France] ; Nicolas Philippe [France] ; Rayan Chikhi [France] ; Mikaël Salson [France] ; Mélina Gallopin [France] ; Marc Gabriel [France] ; Jérémy Le Coz [France] ; Emilie Drouineau [France] ; Thérèse Commes [France] ; Daniel Gautheret [France]Source :
- Genome Biology [ 1474-7596 ] ; 2017.
Abstract
We introduce a
The online version of this article (doi:10.1186/s13059-017-1372-2) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-017-1372-2
PubMed: 29284518
PubMed Central: 5747171
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first="Marc" last="Gabriel">Marc Gabriel</name><affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2171 2558</institution-id><institution-id institution-id-type="GRID">grid.5842.b</institution-id><institution>Institute for Integrative Biology of the Cell, CEA, CNRS,</institution><institution>Université Paris-Sud, Université Paris Saclay,</institution></institution-wrap>Gif sur Yvette, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Gif sur Yvette</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff6"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2284 9388</institution-id><institution-id institution-id-type="GRID">grid.14925.3b</institution-id><institution>Institut de Cancérologie Gustave Roussy Cancer Campus (GRCC), AMMICA, INSERM US23/CNRS UMS3655,</institution></institution-wrap>Villejuif, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Villejuif</wicri:regionArea></affiliation></author><author><name sortKey="Le Coz, Jeremy" sort="Le Coz, Jeremy" uniqKey="Le Coz J" first="Jérémy" last="Le Coz">Jérémy Le Coz</name><affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2171 2558</institution-id><institution-id institution-id-type="GRID">grid.5842.b</institution-id><institution>Institute for Integrative Biology of the Cell, CEA, CNRS,</institution><institution>Université Paris-Sud, Université Paris Saclay,</institution></institution-wrap>Gif sur Yvette, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Gif sur Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Drouineau, Emilie" sort="Drouineau, Emilie" uniqKey="Drouineau E" first="Emilie" last="Drouineau">Emilie Drouineau</name><affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2171 2558</institution-id><institution-id institution-id-type="GRID">grid.5842.b</institution-id><institution>Institute for Integrative Biology of the Cell, CEA, CNRS,</institution><institution>Université Paris-Sud, Université Paris Saclay,</institution></institution-wrap>Gif sur Yvette, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Gif sur Yvette</wicri:regionArea></affiliation></author><author><name sortKey="Commes, Therese" sort="Commes, Therese" uniqKey="Commes T" first="Thérèse" last="Commes">Thérèse Commes</name><affiliation wicri:level="1"><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2097 0141</institution-id><institution-id institution-id-type="GRID">grid.121334.6</institution-id><institution>INSERM U1183 IRMB,</institution><institution>Université de Montpellier,</institution></institution-wrap>Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295 France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2097 0141</institution-id><institution-id institution-id-type="GRID">grid.121334.6</institution-id><institution>Institut de Biologie Computationnelle,</institution><institution>Université Montpellier,</institution></institution-wrap>Montpellier, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Montpellier</wicri:regionArea></affiliation></author><author><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name><affiliation wicri:level="1"><nlm:aff id="Aff5"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2171 2558</institution-id><institution-id institution-id-type="GRID">grid.5842.b</institution-id><institution>Institute for Integrative Biology of the Cell, CEA, CNRS,</institution><institution>Université Paris-Sud, Université Paris Saclay,</institution></institution-wrap>Gif sur Yvette, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Gif sur Yvette</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff6"><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2284 9388</institution-id><institution-id institution-id-type="GRID">grid.14925.3b</institution-id><institution>Institut de Cancérologie Gustave Roussy Cancer Campus (GRCC), AMMICA, INSERM US23/CNRS UMS3655,</institution></institution-wrap>Villejuif, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Villejuif</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1474-7596</idno><idno type="eISSN">1474-760X</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We introduce a <italic>k</italic>-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all <italic>k</italic>-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-017-1372-2) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, C" uniqKey="Zhang C">C Zhang</name></author><author><name sortKey="Zhang, B" uniqKey="Zhang B">B Zhang</name></author><author><name sortKey="Lin, Ll" uniqKey="Lin L">LL Lin</name></author><author><name sortKey="Zhao, S" uniqKey="Zhao S">S Zhao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soneson, C" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id><journal-title-group><journal-title>Genome Biology</journal-title></journal-title-group><issn pub-type="ppub">1474-7596</issn><issn pub-type="epub">1474-760X</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">29284518</article-id><article-id pub-id-type="pmc">5747171</article-id><article-id pub-id-type="publisher-id">1372</article-id><article-id pub-id-type="doi">10.1186/s13059-017-1372-2</article-id><article-categories><subj-group subj-group-type="heading"><subject>Method</subject></subj-group></article-categories><title-group><article-title>DE-kupl: exhaustive capture of biological variation in RNA-seq data through <italic>k</italic>-mer decomposition</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Audoux</surname><given-names>Jérôme</given-names></name><xref ref-type="aff" rid="Aff1">1</xref></contrib><contrib contrib-type="author"><name><surname>Philippe</surname><given-names>Nicolas</given-names></name><xref ref-type="aff" rid="Aff2">2</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Chikhi</surname><given-names>Rayan</given-names></name><xref ref-type="aff" rid="Aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Salson</surname><given-names>Mikaël</given-names></name><xref ref-type="aff" rid="Aff4">4</xref></contrib><contrib contrib-type="author"><name><surname>Gallopin</surname><given-names>Mélina</given-names></name><xref ref-type="aff" rid="Aff5">5</xref></contrib><contrib contrib-type="author"><name><surname>Gabriel</surname><given-names>Marc</given-names></name><xref ref-type="aff" rid="Aff5">5</xref><xref ref-type="aff" rid="Aff6">6</xref></contrib><contrib contrib-type="author"><name><surname>Le Coz</surname><given-names>Jérémy</given-names></name><xref ref-type="aff" rid="Aff5">5</xref></contrib><contrib contrib-type="author"><name><surname>Drouineau</surname><given-names>Emilie</given-names></name><xref ref-type="aff" rid="Aff5">5</xref></contrib><contrib contrib-type="author"><name><surname>Commes</surname><given-names>Thérèse</given-names></name><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref></contrib><contrib contrib-type="author" corresp="yes"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-1508-8469</contrib-id><name><surname>Gautheret</surname><given-names>Daniel</given-names></name><address><email>daniel.gautheret@u-psud.fr</email></address><xref ref-type="aff" rid="Aff5">5</xref><xref ref-type="aff" rid="Aff6">6</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2097 0141</institution-id><institution-id institution-id-type="GRID">grid.121334.6</institution-id><institution>INSERM U1183 IRMB,</institution><institution>Université de Montpellier,</institution></institution-wrap>Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295 France</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2097 0141</institution-id><institution-id institution-id-type="GRID">grid.121334.6</institution-id><institution>Institut de Biologie Computationnelle,</institution><institution>Université Montpellier,</institution></institution-wrap>Montpellier, France</aff><aff id="Aff3"><label>3</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0000 9961 060X</institution-id><institution-id institution-id-type="GRID">grid.157868.5</institution-id><institution>SeqOne, IRMB,</institution><institution>CHRU de Montpellier,</institution></institution-wrap>Hopital St Eloi, Montpellier, France</aff><aff id="Aff4"><label>4</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2112 9282</institution-id><institution-id institution-id-type="GRID">grid.4444.0</institution-id><institution>Univ. Lille, CNRS, Inria,</institution></institution-wrap>UMR 9189 - CRIStAL - F-59000, Lille, France</aff><aff id="Aff5"><label>5</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2171 2558</institution-id><institution-id institution-id-type="GRID">grid.5842.b</institution-id><institution>Institute for Integrative Biology of the Cell, CEA, CNRS,</institution><institution>Université Paris-Sud, Université Paris Saclay,</institution></institution-wrap>Gif sur Yvette, France</aff><aff id="Aff6"><label>6</label><institution-wrap><institution-id institution-id-type="ISNI">0000 0001 2284 9388</institution-id><institution-id institution-id-type="GRID">grid.14925.3b</institution-id><institution>Institut de Cancérologie Gustave Roussy Cancer Campus (GRCC), AMMICA, INSERM US23/CNRS UMS3655,</institution></institution-wrap>Villejuif, France</aff></contrib-group><pub-date pub-type="epub"><day>28</day><month>12</month><year>2017</year></pub-date><pub-date pub-type="pmc-release"><day>28</day><month>12</month><year>2017</year></pub-date><pub-date pub-type="collection"><year>2017</year></pub-date><volume>18</volume><elocation-id>243</elocation-id><history><date date-type="received"><day>1</day><month>6</month><year>2017</year></date><date date-type="accepted"><day>5</day><month>12</month><year>2017</year></date></history><permissions><copyright-statement>© The Author(s) 2017</copyright-statement><license license-type="OpenAccess"><license-p><bold>Open Access</bold> This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise stated.</license-p></license></permissions><abstract id="Abs1"><p>We introduce a <italic>k</italic>-mer-based computational protocol, DE-kupl, for capturing local RNA variation in a set of RNA-seq libraries, independently of a reference genome or transcriptome. DE-kupl extracts all <italic>k</italic>-mers with differential abundance directly from the raw data files. This enables the retrieval of virtually all variation present in an RNA-seq data set. This variation is subsequently assigned to biological events or entities such as differential long non-coding RNAs, splice and polyadenylation variants, introns, repeats, editing or mutation events, and exogenous RNA. Applying DE-kupl to human RNA-seq data sets identified multiple types of novel events, reproducibly across independent RNA-seq experiments.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-017-1372-2) contains supplementary material, which is available to authorized users.</p></sec></abstract><funding-group><award-group><funding-source><institution>Plan Cancer – Systems Biology</institution></funding-source><award-id>#bio2014-04</award-id></award-group><award-group><funding-source><institution>ANR (France)</institution></funding-source><award-id>ANR-10-INBS-0009 (France Génomique)</award-id></award-group></funding-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2017</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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