DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Identifieur interne : 000E39 ( Main/Merge ); précédent : 000E38; suivant : 000E40DE-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.
Descripteurs français
- KwdFr :
- ARN (génétique), ARN antisens, ARN long non codant (génétique), ARN messager (génétique), Allèles, Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Biologie informatique (), Humains, Logiciel, Polyadénylation, Reproductibilité des résultats, Régulation de l'expression des gènes, Séquençage nucléotidique à haut débit, Transcriptome, Variation génétique, Épissage des ARN.
- MESH :
- génétique : ARN, ARN long non codant, ARN messager.
- ARN antisens, Allèles, Analyse de profil d'expression de gènes, Analyse de séquence d'ARN, Biologie informatique, Humains, Logiciel, Polyadénylation, Reproductibilité des résultats, Régulation de l'expression des gènes, Séquençage nucléotidique à haut débit, Transcriptome, Variation génétique, Épissage des ARN.
English descriptors
- KwdEn :
- Alleles, Computational Biology (methods), Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Polyadenylation, RNA (genetics), RNA Splicing, RNA, Antisense, RNA, Long Noncoding (genetics), RNA, Messenger (genetics), Reproducibility of Results, Sequence Analysis, RNA, Software, Transcriptome.
- MESH :
- chemical , genetics : RNA, RNA, Long Noncoding, RNA, Messenger.
- methods : Computational Biology.
- Alleles, Gene Expression Profiling, Gene Expression Regulation, Genetic Variation, High-Throughput Nucleotide Sequencing, Humans, Polyadenylation, RNA Splicing, RNA, Antisense, Reproducibility of Results, Sequence Analysis, RNA, Software, Transcriptome.
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
Links toward previous steps (curation, corpus...)
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- to stream PubMed, to step Curation: 000A36
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Links to Exploration step
PMC:5747171Le document en format XML
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-mer decomposition</title>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DE-kupl: exhaustive capture of biological variation in RNA-seq data through <italic>k</italic>
-mer decomposition</title>
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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>
<placeName><region type="region">Occitanie (région administrative)</region>
<region type="old region">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
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<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>
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</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>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term>
<term>Computational Biology (methods)</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation</term>
<term>Genetic Variation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Polyadenylation</term>
<term>RNA (genetics)</term>
<term>RNA Splicing</term>
<term>RNA, Antisense</term>
<term>RNA, Long Noncoding (genetics)</term>
<term>RNA, Messenger (genetics)</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, RNA</term>
<term>Software</term>
<term>Transcriptome</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ARN (génétique)</term>
<term>ARN antisens</term>
<term>ARN long non codant (génétique)</term>
<term>ARN messager (génétique)</term>
<term>Allèles</term>
<term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ARN</term>
<term>Biologie informatique ()</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Polyadénylation</term>
<term>Reproductibilité des résultats</term>
<term>Régulation de l'expression des gènes</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Transcriptome</term>
<term>Variation génétique</term>
<term>Épissage des ARN</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA</term>
<term>RNA, Long Noncoding</term>
<term>RNA, Messenger</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN</term>
<term>ARN long non codant</term>
<term>ARN messager</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Alleles</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation</term>
<term>Genetic Variation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Polyadenylation</term>
<term>RNA Splicing</term>
<term>RNA, Antisense</term>
<term>Reproducibility of Results</term>
<term>Sequence Analysis, RNA</term>
<term>Software</term>
<term>Transcriptome</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ARN antisens</term>
<term>Allèles</term>
<term>Analyse de profil d'expression de gènes</term>
<term>Analyse de séquence d'ARN</term>
<term>Biologie informatique</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Polyadénylation</term>
<term>Reproductibilité des résultats</term>
<term>Régulation de l'expression des gènes</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Transcriptome</term>
<term>Variation génétique</term>
<term>Épissage des ARN</term>
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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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