DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition
Identifieur interne : 000E36 ( Main/Exploration ); précédent : 000E35; suivant : 000E37DE-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
Affiliations:
- France
- Hauts-de-France, Languedoc-Roussillon, Nord-Pas-de-Calais, Occitanie (région administrative)
- Lille, Montpellier
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000367
- to stream Pmc, to step Curation: 000367
- to stream Pmc, to step Checkpoint: 000894
- to stream PubMed, to step Corpus: 000A36
- to stream PubMed, to step Curation: 000A36
- to stream PubMed, to step Checkpoint: 000D47
- to stream Ncbi, to step Merge: 001C97
- to stream Ncbi, to step Curation: 001C97
- to stream Ncbi, to step Checkpoint: 001C97
- to stream Main, to step Merge: 000E39
- to stream Main, to step Curation: 000E36
Le document en format XML
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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><placeName><region type="region">Occitanie (région administrative)</region><region type="old region">Languedoc-Roussillon</region><settlement type="city">Montpellier</settlement></placeName></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><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></keywords></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" uniqKey="Soneson C">C Soneson</name></author><author><name sortKey="Matthes, Kl" uniqKey="Matthes K">KL Matthes</name></author><author><name sortKey="Nowicka, M" uniqKey="Nowicka M">M Nowicka</name></author><author><name sortKey="Law, Cw" uniqKey="Law C">CW Law</name></author><author><name sortKey="Robinson, Md" uniqKey="Robinson M">MD Robinson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Teng, M" uniqKey="Teng M">M Teng</name></author><author><name sortKey="Love, Mi" uniqKey="Love M">MI Love</name></author><author><name sortKey="Davis, Ca" uniqKey="Davis C">CA Davis</name></author><author><name sortKey="Djebali, S" uniqKey="Djebali S">S Djebali</name></author><author><name sortKey="Dobin, A" uniqKey="Dobin A">A Dobin</name></author><author><name sortKey="Graveley, Br" uniqKey="Graveley B">BR Graveley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanitz, A" uniqKey="Kanitz A">A Kanitz</name></author><author><name sortKey="Gypas, F" uniqKey="Gypas F">F Gypas</name></author><author><name sortKey="Gruber, Aj" uniqKey="Gruber A">AJ Gruber</name></author><author><name sortKey="Gruber, Ar" uniqKey="Gruber A">AR Gruber</name></author><author><name sortKey="Martin, G" uniqKey="Martin G">G Martin</name></author><author><name sortKey="Zavolan, M" uniqKey="Zavolan M">M Zavolan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Middleton, R" uniqKey="Middleton R">R Middleton</name></author><author><name sortKey="Gao, D" uniqKey="Gao D">D Gao</name></author><author><name sortKey="Thomas, A" uniqKey="Thomas A">A Thomas</name></author><author><name sortKey="Singh, B" uniqKey="Singh B">B Singh</name></author><author><name sortKey="Au, A" uniqKey="Au A">A Au</name></author><author><name sortKey="Wong, Jj" uniqKey="Wong J">JJ Wong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, D" uniqKey="Kim D">D Kim</name></author><author><name sortKey="Pertea, G" uniqKey="Pertea G">G Pertea</name></author><author><name sortKey="Trapnell, C" uniqKey="Trapnell C">C Trapnell</name></author><author><name sortKey="Pimentel, H" uniqKey="Pimentel H">H Pimentel</name></author><author><name sortKey="Kelley, R" uniqKey="Kelley R">R Kelley</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Benelli, M" uniqKey="Benelli M">M Benelli</name></author><author><name sortKey="Pescucci, C" uniqKey="Pescucci C">C Pescucci</name></author><author><name sortKey="Marseglia, G" uniqKey="Marseglia G">G Marseglia</name></author><author><name sortKey="Severgnini, M" uniqKey="Severgnini M">M Severgnini</name></author><author><name sortKey="Torricelli, F" uniqKey="Torricelli F">F Torricelli</name></author><author><name sortKey="Magi, A" uniqKey="Magi A">A Magi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Memczak, S" uniqKey="Memczak S">S Memczak</name></author><author><name sortKey="Jens, M" uniqKey="Jens M">M Jens</name></author><author><name sortKey="Elefsinioti, A" uniqKey="Elefsinioti A">A Elefsinioti</name></author><author><name sortKey="Torti, F" uniqKey="Torti F">F Torti</name></author><author><name sortKey="Krueger, J" uniqKey="Krueger J">J Krueger</name></author><author><name sortKey="Rybak, A" uniqKey="Rybak A">A Rybak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deelen, P" uniqKey="Deelen P">P Deelen</name></author><author><name sortKey="Zhernakova, Dv" uniqKey="Zhernakova D">DV Zhernakova</name></author><author><name sortKey="De Haan, M" uniqKey="De Haan M">M de Haan</name></author><author><name sortKey="Van Der Sijde, M" uniqKey="Van Der Sijde M">M van der Sijde</name></author><author><name sortKey="Bonder, Mj" uniqKey="Bonder M">MJ Bonder</name></author><author><name sortKey="Karjalainen, J" uniqKey="Karjalainen J">J Karjalainen</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Weinstein, Jn" uniqKey="Weinstein J">JN Weinstein</name></author><author><name sortKey="Collisson, Ea" uniqKey="Collisson E">EA Collisson</name></author><author><name sortKey="Mills, Gb" uniqKey="Mills G">GB Mills</name></author><author><name sortKey="Shaw, Krm" uniqKey="Shaw K">KRM Shaw</name></author><author><name sortKey="Ozenberger, Ba" uniqKey="Ozenberger B">BA Ozenberger</name></author><author><name sortKey="Ellrott, K" uniqKey="Ellrott K">K Ellrott</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Rodriguez, Jm" uniqKey="Rodriguez J">JM Rodriguez</name></author><author><name sortKey="Maietta, P" uniqKey="Maietta P">P Maietta</name></author><author><name sortKey="Ezkurdia, I" uniqKey="Ezkurdia I">I Ezkurdia</name></author><author><name sortKey="Pietrelli, A" uniqKey="Pietrelli A">A Pietrelli</name></author><author><name sortKey="Wesselink, Jj" uniqKey="Wesselink J">JJ Wesselink</name></author><author><name sortKey="Lopez, G" uniqKey="Lopez G">G Lopez</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Benjamini, Y" uniqKey="Benjamini Y">Y Benjamini</name></author><author><name sortKey="Hochberg, Y" uniqKey="Hochberg Y">Y Hochberg</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><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>Pour manipuler ce document sous Unix (Dilib)
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