DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Identifieur interne : 000894 ( Pmc/Checkpoint ); précédent : 000893; suivant : 000895DE-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
Affiliations:
- France
- Hauts-de-France, Languedoc-Roussillon, Nord-Pas-de-Calais, Occitanie (région administrative)
- Lille, Montpellier
Links toward previous steps (curation, corpus...)
Links to Exploration step
PMC:5747171Le document en format XML
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-mer decomposition</title>
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-mer decomposition</title>
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<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>
<affiliations><list><country><li>France</li>
</country>
<region><li>Hauts-de-France</li>
<li>Languedoc-Roussillon</li>
<li>Nord-Pas-de-Calais</li>
<li>Occitanie (région administrative)</li>
</region>
<settlement><li>Lille</li>
<li>Montpellier</li>
</settlement>
</list>
<tree><country name="France"><region name="Occitanie (région administrative)"><name sortKey="Audoux, Jerome" sort="Audoux, Jerome" uniqKey="Audoux J" first="Jérôme" last="Audoux">Jérôme Audoux</name>
</region>
<name sortKey="Chikhi, Rayan" sort="Chikhi, Rayan" uniqKey="Chikhi R" first="Rayan" last="Chikhi">Rayan Chikhi</name>
<name sortKey="Commes, Therese" sort="Commes, Therese" uniqKey="Commes T" first="Thérèse" last="Commes">Thérèse Commes</name>
<name sortKey="Commes, Therese" sort="Commes, Therese" uniqKey="Commes T" first="Thérèse" last="Commes">Thérèse Commes</name>
<name sortKey="Drouineau, Emilie" sort="Drouineau, Emilie" uniqKey="Drouineau E" first="Emilie" last="Drouineau">Emilie Drouineau</name>
<name sortKey="Gabriel, Marc" sort="Gabriel, Marc" uniqKey="Gabriel M" first="Marc" last="Gabriel">Marc Gabriel</name>
<name sortKey="Gabriel, Marc" sort="Gabriel, Marc" uniqKey="Gabriel M" first="Marc" last="Gabriel">Marc Gabriel</name>
<name sortKey="Gallopin, Melina" sort="Gallopin, Melina" uniqKey="Gallopin M" first="Mélina" last="Gallopin">Mélina Gallopin</name>
<name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name>
<name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name>
<name sortKey="Le Coz, Jeremy" sort="Le Coz, Jeremy" uniqKey="Le Coz J" first="Jérémy" last="Le Coz">Jérémy Le Coz</name>
<name sortKey="Philippe, Nicolas" sort="Philippe, Nicolas" uniqKey="Philippe N" first="Nicolas" last="Philippe">Nicolas Philippe</name>
<name sortKey="Philippe, Nicolas" sort="Philippe, Nicolas" uniqKey="Philippe N" first="Nicolas" last="Philippe">Nicolas Philippe</name>
<name sortKey="Salson, Mikael" sort="Salson, Mikael" uniqKey="Salson M" first="Mikaël" last="Salson">Mikaël Salson</name>
</country>
</tree>
</affiliations>
</record>
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