DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
Identifieur interne : 000D47 ( PubMed/Checkpoint ); précédent : 000D46; suivant : 000D48DE-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 [ 1474-760X ] ; 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 k-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 k-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.
DOI: 10.1186/s13059-017-1372-2
PubMed: 29284518
Affiliations:
- France
- Hauts-de-France, Languedoc-Roussillon, Nord-Pas-de-Calais, Occitanie (région administrative), Île-de-France
- Gif-sur-Yvette, Lille, Montpellier
- Université Paris-Sud
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:29284518Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.</title><author><name sortKey="Audoux, Jerome" sort="Audoux, Jerome" uniqKey="Audoux J" first="Jérôme" last="Audoux">Jérôme Audoux</name><affiliation wicri:level="3"><nlm:affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Philippe, Nicolas" sort="Philippe, Nicolas" uniqKey="Philippe N" first="Nicolas" last="Philippe">Nicolas Philippe</name><affiliation wicri:level="3"><nlm:affiliation>Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut de Biologie Computationnelle, Université Montpellier, 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></author><author><name sortKey="Chikhi, Rayan" sort="Chikhi, Rayan" uniqKey="Chikhi R" first="Rayan" last="Chikhi">Rayan Chikhi</name><affiliation wicri:level="3"><nlm:affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Lille</settlement></placeName></affiliation></author><author><name sortKey="Salson, Mikael" sort="Salson, Mikael" uniqKey="Salson M" first="Mikaël" last="Salson">Mikaël Salson</name><affiliation wicri:level="3"><nlm:affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Lille</settlement></placeName></affiliation></author><author><name sortKey="Gallopin, Melina" sort="Gallopin, Melina" uniqKey="Gallopin M" first="Mélina" last="Gallopin">Mélina Gallopin</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Gabriel, Marc" sort="Gabriel, Marc" uniqKey="Gabriel M" first="Marc" last="Gabriel">Marc Gabriel</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></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="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Drouineau, Emilie" sort="Drouineau, Emilie" uniqKey="Drouineau E" first="Emilie" last="Drouineau">Emilie Drouineau</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Commes, Therese" sort="Commes, Therese" uniqKey="Commes T" first="Thérèse" last="Commes">Thérèse Commes</name><affiliation wicri:level="3"><nlm:affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France. daniel.gautheret@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29284518</idno><idno type="pmid">29284518</idno><idno type="doi">10.1186/s13059-017-1372-2</idno><idno type="wicri:Area/PubMed/Corpus">000A36</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000A36</idno><idno type="wicri:Area/PubMed/Curation">000A36</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000A36</idno><idno type="wicri:Area/PubMed/Checkpoint">000D47</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000D47</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.</title><author><name sortKey="Audoux, Jerome" sort="Audoux, Jerome" uniqKey="Audoux J" first="Jérôme" last="Audoux">Jérôme Audoux</name><affiliation wicri:level="3"><nlm:affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Philippe, Nicolas" sort="Philippe, Nicolas" uniqKey="Philippe N" first="Nicolas" last="Philippe">Nicolas Philippe</name><affiliation wicri:level="3"><nlm:affiliation>Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut de Biologie Computationnelle, Université Montpellier, 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></author><author><name sortKey="Chikhi, Rayan" sort="Chikhi, Rayan" uniqKey="Chikhi R" first="Rayan" last="Chikhi">Rayan Chikhi</name><affiliation wicri:level="3"><nlm:affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Lille</settlement></placeName></affiliation></author><author><name sortKey="Salson, Mikael" sort="Salson, Mikael" uniqKey="Salson M" first="Mikaël" last="Salson">Mikaël Salson</name><affiliation wicri:level="3"><nlm:affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Nord-Pas-de-Calais</region><settlement type="city">Lille</settlement></placeName></affiliation></author><author><name sortKey="Gallopin, Melina" sort="Gallopin, Melina" uniqKey="Gallopin M" first="Mélina" last="Gallopin">Mélina Gallopin</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Gabriel, Marc" sort="Gabriel, Marc" uniqKey="Gabriel M" first="Marc" last="Gabriel">Marc Gabriel</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></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="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Drouineau, Emilie" sort="Drouineau, Emilie" uniqKey="Drouineau E" first="Emilie" last="Drouineau">Emilie Drouineau</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author><author><name sortKey="Commes, Therese" sort="Commes, Therese" uniqKey="Commes T" first="Thérèse" last="Commes">Thérèse Commes</name><affiliation wicri:level="3"><nlm:affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295</wicri:regionArea><placeName><region type="region" nuts="2">Occitanie (région administrative)</region><region type="old region" nuts="2">Languedoc-Roussillon</region></placeName></affiliation></author><author><name sortKey="Gautheret, Daniel" sort="Gautheret, Daniel" uniqKey="Gautheret D" first="Daniel" last="Gautheret">Daniel Gautheret</name><affiliation wicri:level="4"><nlm:affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France. daniel.gautheret@u-psud.fr.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette</wicri:regionArea><placeName><region type="region" nuts="2">Île-de-France</region><settlement type="city">Gif-sur-Yvette</settlement></placeName><orgName type="university">Université Paris-Sud</orgName></affiliation></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2017" type="published">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">We introduce a k-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 k-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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29284518</PMID><DateCompleted><Year>2018</Year><Month>08</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>12</Month><Day>28</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol.</ISOAbbreviation></Journal><ArticleTitle>DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.</ArticleTitle><Pagination><MedlinePgn>243</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13059-017-1372-2</ELocationID><Abstract><AbstractText>We introduce a k-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 k-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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Audoux</LastName><ForeName>Jérôme</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Philippe</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>SeqOne, IRMB, CHRU de Montpellier, Hopital St Eloi, Montpellier, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chikhi</LastName><ForeName>Rayan</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salson</LastName><ForeName>Mikaël</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Univ. Lille, CNRS, Inria, UMR 9189 - CRIStAL - F-59000, Lille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gallopin</LastName><ForeName>Mélina</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gabriel</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Cancérologie Gustave Roussy Cancer Campus (GRCC), AMMICA, INSERM US23/CNRS UMS3655, Villejuif, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Le Coz</LastName><ForeName>Jérémy</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Drouineau</LastName><ForeName>Emilie</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Commes</LastName><ForeName>Thérèse</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>INSERM U1183 IRMB, Université de Montpellier, Hopital St Eloi, 80 avenue Augustin Fliche, Montpellier, 34295, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gautheret</LastName><ForeName>Daniel</ForeName><Initials>D</Initials><Identifier Source="ORCID">0000-0002-1508-8469</Identifier><AffiliationInfo><Affiliation>Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France. daniel.gautheret@u-psud.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut de Cancérologie Gustave Roussy Cancer Campus (GRCC), AMMICA, INSERM US23/CNRS UMS3655, Villejuif, France. daniel.gautheret@u-psud.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>#bio2014-04</GrantID><Agency>Plan Cancer - Systems Biology</Agency><Country>International</Country></Grant><Grant><GrantID>ANR-10-INBS-0009 (France Génomique)</GrantID><Agency>ANR (France)</Agency><Country>International</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>12</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol</MedlineTA><NlmUniqueID>100960660</NlmUniqueID><ISSNLinking>1474-7596</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D016372">RNA, Antisense</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D062085">RNA, Long Noncoding</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>63231-63-0</RegistryNumber><NameOfSubstance UI="D012313">RNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="N">Gene Expression Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026723" MajorTopicYN="N">Polyadenylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012313" MajorTopicYN="N">RNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012326" MajorTopicYN="N">RNA Splicing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016372" MajorTopicYN="N">RNA, Antisense</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D062085" MajorTopicYN="N">RNA, Long Noncoding</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>06</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>12</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>12</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>12</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>8</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29284518</ArticleId><ArticleId IdType="doi">10.1186/s13059-017-1372-2</ArticleId><ArticleId IdType="pii">10.1186/s13059-017-1372-2</ArticleId><ArticleId IdType="pmc">PMC5747171</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7</Citation><ArticleIdList><ArticleId IdType="pubmed">23161672</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Biochem. 2010;79:321-49</Citation><ArticleIdList><ArticleId IdType="pubmed">20192758</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2016 May;34(5):525-7</Citation><ArticleIdList><ArticleId IdType="pubmed">27043002</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2016 Jan 26;17 :12</Citation><ArticleIdList><ArticleId IdType="pubmed">26813113</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2017 Mar 15;18(1):51</Citation><ArticleIdList><ArticleId IdType="pubmed">28298237</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2017 Nov 13;:null</Citation><ArticleIdList><ArticleId IdType="pubmed">29140475</ArticleId></ArticleIdList></Reference><Reference><Citation>Biostatistics. 2014 Jul;15(3):413-26</Citation><ArticleIdList><ArticleId IdType="pubmed">24398039</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D975-9</Citation><ArticleIdList><ArticleId IdType="pubmed">24297256</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(1):e30377</Citation><ArticleIdList><ArticleId IdType="pubmed">22276185</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2011 Aug 04;12:323</Citation><ArticleIdList><ArticleId IdType="pubmed">21816040</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2015 Jan 23;347(6220):1260419</Citation><ArticleIdList><ArticleId IdType="pubmed">25613900</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Comput Biol. 2015 Jul 09;11(7):e1004274</Citation><ArticleIdList><ArticleId IdType="pubmed">26158448</ArticleId></ArticleIdList></Reference><Reference><Citation>Genomics. 2009 Aug;94(2):83-8</Citation><ArticleIdList><ArticleId IdType="pubmed">19446021</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2013 Apr 25;14(4):R36</Citation><ArticleIdList><ArticleId IdType="pubmed">23618408</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2013 Mar 21;495(7441):333-8</Citation><ArticleIdList><ArticleId IdType="pubmed">23446348</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2010;11(10):R106</Citation><ArticleIdList><ArticleId IdType="pubmed">20979621</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2014 Feb 03;15(2):R29</Citation><ArticleIdList><ArticleId IdType="pubmed">24485249</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2010 Aug;284(2):95-103</Citation><ArticleIdList><ArticleId IdType="pubmed">20596726</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2016 Sep 1;32(17 ):i538-i544</Citation><ArticleIdList><ArticleId IdType="pubmed">27587672</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2013 Jan 1;29(1):15-21</Citation><ArticleIdList><ArticleId IdType="pubmed">23104886</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Mar 15;27(6):764-70</Citation><ArticleIdList><ArticleId IdType="pubmed">21217122</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2010 May;28(5):511-5</Citation><ArticleIdList><ArticleId IdType="pubmed">20436464</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2016 Apr 23;17 :74</Citation><ArticleIdList><ArticleId IdType="pubmed">27107712</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cancer Res. 2017 Sep;15(9):1206-1220</Citation><ArticleIdList><ArticleId IdType="pubmed">28584021</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2013 Aug;8(8):1494-512</Citation><ArticleIdList><ArticleId IdType="pubmed">23845962</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 May 15;29(7):644-52</Citation><ArticleIdList><ArticleId IdType="pubmed">21572440</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2015 Feb;16(2):98-112</Citation><ArticleIdList><ArticleId IdType="pubmed">25534324</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2010 Sep 03;5(9):e12336</Citation><ArticleIdList><ArticleId IdType="pubmed">20838429</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2012 Sep;22(9):1760-74</Citation><ArticleIdList><ArticleId IdType="pubmed">22955987</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Mar 15;26(6):841-2</Citation><ArticleIdList><ArticleId IdType="pubmed">20110278</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Apr 1;26(7):873-81</Citation><ArticleIdList><ArticleId IdType="pubmed">20147302</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Dec 15;28(24):3232-9</Citation><ArticleIdList><ArticleId IdType="pubmed">23093608</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 Jan;29(1):24-6</Citation><ArticleIdList><ArticleId IdType="pubmed">21221095</ArticleId></ArticleIdList></Reference><Reference><Citation>RNA Biol. 2016;13(1):59-67</Citation><ArticleIdList><ArticleId IdType="pubmed">26849165</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Mol Cell Biol. 2016 Apr;17 (4):205-11</Citation><ArticleIdList><ArticleId IdType="pubmed">26908011</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2016 Jun 20;17 (1):132</Citation><ArticleIdList><ArticleId IdType="pubmed">27323842</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2013 Jan;41(Database issue):D991-5</Citation><ArticleIdList><ArticleId IdType="pubmed">23193258</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2017 Apr;14 (4):417-419</Citation><ArticleIdList><ArticleId IdType="pubmed">28263959</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Protoc. 2012 Mar 01;7(3):562-78</Citation><ArticleIdList><ArticleId IdType="pubmed">22383036</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Commun. 2017 Jul 5;8(1):59</Citation><ArticleIdList><ArticleId IdType="pubmed">28680106</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Genet. 2013 Oct;45(10):1113-20</Citation><ArticleIdList><ArticleId IdType="pubmed">24071849</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2017 Aug 7;18(1):583</Citation><ArticleIdList><ArticleId IdType="pubmed">28784092</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5</Citation><ArticleIdList><ArticleId IdType="pubmed">22537044</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2015 Jul 23;16:150</Citation><ArticleIdList><ArticleId IdType="pubmed">26201343</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2009 Dec 15;10:421</Citation><ArticleIdList><ArticleId IdType="pubmed">20003500</ArticleId></ArticleIdList></Reference><Reference><Citation>Pac Symp Biocomput. 2015;:347-58</Citation><ArticleIdList><ArticleId IdType="pubmed">25592595</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Oct 1;28(19):2520-2</Citation><ArticleIdList><ArticleId IdType="pubmed">22908215</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2017 Dec 15;33(24):4033-4040</Citation><ArticleIdList><ArticleId IdType="pubmed">27592709</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Med. 2015 Mar 27;7(1):30</Citation><ArticleIdList><ArticleId IdType="pubmed">25954321</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2013 Apr;31(4):325-30</Citation><ArticleIdList><ArticleId IdType="pubmed">23475072</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 2016 May 16;36(11):1704-19</Citation><ArticleIdList><ArticleId IdType="pubmed">27044866</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2014;15(12):550</Citation><ArticleIdList><ArticleId IdType="pubmed">25516281</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><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><li>Île-de-France</li></region><settlement><li>Gif-sur-Yvette</li><li>Lille</li><li>Montpellier</li></settlement><orgName><li>Université Paris-Sud</li></orgName></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="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="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="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="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)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000D47 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 000D47 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:29284518
|texte= DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:29284518" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |