IRFinder: assessing the impact of intron retention on mammalian gene expression.
Identifieur interne : 000A52 ( PubMed/Checkpoint ); précédent : 000A51; suivant : 000A53IRFinder: assessing the impact of intron retention on mammalian gene expression.
Auteurs : Robert Middleton [Australie] ; Dadi Gao [Australie] ; Aubin Thomas [France] ; Babita Singh [Espagne] ; Amy Au [Australie] ; Justin J-L Wong [Australie] ; Alexandra Bomane [France] ; Bertrand Cosson [France] ; Eduardo Eyras [Espagne] ; John E J. Rasko [Australie] ; William Ritchie [Australie]Source :
- Genome biology [ 1474-760X ] ; 2017.
Descripteurs français
- KwdFr :
- Animaux, Biologie informatique (), Cycle cellulaire (génétique), Différenciation cellulaire (génétique), Exons, Humains, Introns, Logiciel, Motifs nucléotidiques, Protéines de liaison à l'ARN (métabolisme), Régulation de l'expression des gènes, Sites de fixation, Épissage alternatif, Épissage des ARN.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : RNA-Binding Proteins.
- genetics : Cell Cycle, Cell Differentiation.
- methods : Computational Biology.
- Alternative Splicing, Animals, Binding Sites, Exons, Gene Expression Regulation, Humans, Introns, Nucleotide Motifs, RNA Splicing, Software.
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
DOI: 10.1186/s13059-017-1184-4
PubMed: 28298237
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:28298237Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">IRFinder: assessing the impact of intron retention on mammalian gene expression.</title><author><name sortKey="Middleton, Robert" sort="Middleton, Robert" uniqKey="Middleton R" first="Robert" last="Middleton">Robert Middleton</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Thomas, Aubin" sort="Thomas, Aubin" uniqKey="Thomas A" first="Aubin" last="Thomas">Aubin Thomas</name><affiliation wicri:level="1"><nlm:affiliation>CNRS, UPR 1142, Montpellier, 34094, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, UPR 1142, Montpellier, 34094</wicri:regionArea><wicri:noRegion>34094</wicri:noRegion><wicri:noRegion>34094</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Babita" sort="Singh, Babita" uniqKey="Singh B" first="Babita" last="Singh">Babita Singh</name><affiliation wicri:level="3"><nlm:affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName></affiliation></author><author><name sortKey="Au, Amy" sort="Au, Amy" uniqKey="Au A" first="Amy" last="Au">Amy Au</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Bomane, Alexandra" sort="Bomane, Alexandra" uniqKey="Bomane A" first="Alexandra" last="Bomane">Alexandra Bomane</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris</wicri:regionArea><placeName><settlement type="city">Paris</settlement><region type="région" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Cosson, Bertrand" sort="Cosson, Bertrand" uniqKey="Cosson B" first="Bertrand" last="Cosson">Bertrand Cosson</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris</wicri:regionArea><placeName><settlement type="city">Paris</settlement><region type="région" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Eyras, Eduardo" sort="Eyras, Eduardo" uniqKey="Eyras E" first="Eduardo" last="Eyras">Eduardo Eyras</name><affiliation wicri:level="3"><nlm:affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName></affiliation></author><author><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E J" last="Rasko">John E J. Rasko</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. william.ritchie@igh.cnrs.fr.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28298237</idno><idno type="pmid">28298237</idno><idno type="doi">10.1186/s13059-017-1184-4</idno><idno type="wicri:Area/PubMed/Corpus">000F24</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000F24</idno><idno type="wicri:Area/PubMed/Curation">000F21</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000F21</idno><idno type="wicri:Area/PubMed/Checkpoint">000F21</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000F21</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">IRFinder: assessing the impact of intron retention on mammalian gene expression.</title><author><name sortKey="Middleton, Robert" sort="Middleton, Robert" uniqKey="Middleton R" first="Robert" last="Middleton">Robert Middleton</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Thomas, Aubin" sort="Thomas, Aubin" uniqKey="Thomas A" first="Aubin" last="Thomas">Aubin Thomas</name><affiliation wicri:level="1"><nlm:affiliation>CNRS, UPR 1142, Montpellier, 34094, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CNRS, UPR 1142, Montpellier, 34094</wicri:regionArea><wicri:noRegion>34094</wicri:noRegion><wicri:noRegion>34094</wicri:noRegion></affiliation></author><author><name sortKey="Singh, Babita" sort="Singh, Babita" uniqKey="Singh B" first="Babita" last="Singh">Babita Singh</name><affiliation wicri:level="3"><nlm:affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName></affiliation></author><author><name sortKey="Au, Amy" sort="Au, Amy" uniqKey="Au A" first="Amy" last="Au">Amy Au</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Bomane, Alexandra" sort="Bomane, Alexandra" uniqKey="Bomane A" first="Alexandra" last="Bomane">Alexandra Bomane</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris</wicri:regionArea><placeName><settlement type="city">Paris</settlement><region type="région" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Cosson, Bertrand" sort="Cosson, Bertrand" uniqKey="Cosson B" first="Bertrand" last="Cosson">Bertrand Cosson</name><affiliation wicri:level="3"><nlm:affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris</wicri:regionArea><placeName><settlement type="city">Paris</settlement><region type="région" nuts="2">Île-de-France</region></placeName></affiliation></author><author><name sortKey="Eyras, Eduardo" sort="Eyras, Eduardo" uniqKey="Eyras E" first="Eduardo" last="Eyras">Eduardo Eyras</name><affiliation wicri:level="3"><nlm:affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</nlm:affiliation><country xml:lang="fr">Espagne</country><wicri:regionArea>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona</wicri:regionArea><placeName><settlement type="city">Barcelone</settlement><region nuts="2" type="region">Catalogne</region></placeName></affiliation></author><author><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E J" last="Rasko">John E J. Rasko</name><affiliation wicri:level="1"><nlm:affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></affiliation></author><author><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><affiliation wicri:level="1"><nlm:affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. william.ritchie@igh.cnrs.fr.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050</wicri:regionArea><wicri:noRegion>2050</wicri:noRegion></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>Alternative Splicing</term><term>Animals</term><term>Binding Sites</term><term>Cell Cycle (genetics)</term><term>Cell Differentiation (genetics)</term><term>Computational Biology (methods)</term><term>Exons</term><term>Gene Expression Regulation</term><term>Humans</term><term>Introns</term><term>Nucleotide Motifs</term><term>RNA Splicing</term><term>RNA-Binding Proteins (metabolism)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Biologie informatique ()</term><term>Cycle cellulaire (génétique)</term><term>Différenciation cellulaire (génétique)</term><term>Exons</term><term>Humains</term><term>Introns</term><term>Logiciel</term><term>Motifs nucléotidiques</term><term>Protéines de liaison à l'ARN (métabolisme)</term><term>Régulation de l'expression des gènes</term><term>Sites de fixation</term><term>Épissage alternatif</term><term>Épissage des ARN</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA-Binding Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Cycle</term><term>Cell Differentiation</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Cycle cellulaire</term><term>Différenciation cellulaire</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines de liaison à l'ARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alternative Splicing</term><term>Animals</term><term>Binding Sites</term><term>Exons</term><term>Gene Expression Regulation</term><term>Humans</term><term>Introns</term><term>Nucleotide Motifs</term><term>RNA Splicing</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Exons</term><term>Humains</term><term>Introns</term><term>Logiciel</term><term>Motifs nucléotidiques</term><term>Régulation de l'expression des gènes</term><term>Sites de fixation</term><term>Épissage alternatif</term><term>Épissage des ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28298237</PMID><DateCreated><Year>2017</Year><Month>03</Month><Day>16</Day></DateCreated><DateCompleted><Year>2017</Year><Month>07</Month><Day>07</Day></DateCompleted><DateRevised><Year>2017</Year><Month>07</Month><Day>07</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>Mar</Month><Day>15</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol.</ISOAbbreviation></Journal><ArticleTitle>IRFinder: assessing the impact of intron retention on mammalian gene expression.</ArticleTitle><Pagination><MedlinePgn>51</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13059-017-1184-4</ELocationID><Abstract><AbstractText>Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Middleton</LastName><ForeName>Robert</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Dadi</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Boston & Harvard Medical School, Boston, MA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thomas</LastName><ForeName>Aubin</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>CNRS, UPR 1142, Montpellier, 34094, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Babita</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Au</LastName><ForeName>Amy</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Justin J-L</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bomane</LastName><ForeName>Alexandra</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cosson</LastName><ForeName>Bertrand</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eyras</LastName><ForeName>Eduardo</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, E08010, Barcelona, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rasko</LastName><ForeName>John E J</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ritchie</LastName><ForeName>William</ForeName><Initials>W</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8162-1439</Identifier><AffiliationInfo><Affiliation>Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. william.ritchie@igh.cnrs.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>CNRS, UPR 1142, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>CNRS, UMR 5203, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>03</Month><Day>15</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="D016601">RNA-Binding Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Nat Methods. 2015 Feb;12(2):147-53</RefSource><PMID Version="1">25486063</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>FEBS J. 2011 Sep;278(18):3246-55</RefSource><PMID Version="1">21794093</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12813-8</RefSource><PMID Version="1">16123126</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genes Dev. 2015 Jan 1;29(1):63-80</RefSource><PMID Version="1">25561496</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Syst Biol. 2014 Nov 17;10:760</RefSource><PMID Version="1">25403753</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Methods. 2010 Dec;7(12):1009-15</RefSource><PMID Version="1">21057496</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Science. 2015 Jan 23;347(6220):1260419</RefSource><PMID Version="1">25613900</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2015 Nov;47(11):1242-8</RefSource><PMID Version="1">26437032</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Bioinformatics. 2013 Jan 1;29(1):15-21</RefSource><PMID Version="1">23104886</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Neurosci. 2011 Jul 6;31(27):9789-99</RefSource><PMID Version="1">21734270</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2012 Oct;22(10):2008-17</RefSource><PMID Version="1">22722343</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Blood. 2016 Mar 9;:null</RefSource><PMID Version="1">26962124</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Biol. 2012 May 24;13(5):R35</RefSource><PMID Version="1">22624609</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Elife. 2015 Jan 07;4:null</RefSource><PMID Version="1">25564732</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2014 Dec 11;516(7530):198-206</RefSource><PMID Version="1">25503233</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2016 Oct 14;44(18):8933-8950</RefSource><PMID Version="1">27317697</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2014 Nov;24(11):1774-86</RefSource><PMID Version="1">25258385</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Biol Chem. 2005 Jul 1;280(26):24371-9</RefSource><PMID Version="1">15863505</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cell. 2013 Aug 1;154(3):583-95</RefSource><PMID Version="1">23911323</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2016 Jan 29;44(2):838-51</RefSource><PMID Version="1">26531823</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cell. 2012 Nov 9;151(4):750-64</RefSource><PMID Version="1">23084401</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Neuron. 2011 Mar 10;69(5):877-84</RefSource><PMID Version="1">21382548</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Curr Opin Genet Dev. 2011 Aug;21(4):422-30</RefSource><PMID Version="1">21550797</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Sci Rep. 2012;2:603</RefSource><PMID Version="1">22934129</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2016 Aug 19;44(14):6817-29</RefSource><PMID Version="1">27369383</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genes Dev. 2012 Jun 1;26(11):1209-23</RefSource><PMID Version="1">22661231</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Biotechnol. 2015 Nov;33(11):1173-81</RefSource><PMID Version="1">26501951</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Proc Natl Acad Sci U S A. 1976 Jan;73(1):183-7</RefSource><PMID Version="1">1061114</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2007 Apr 19;446(7138):926-9</RefSource><PMID Version="1">17361132</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Genet. 2008 Dec;40(12):1413-5</RefSource><PMID Version="1">18978789</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>FASEB J. 2006 Dec;20(14):2588-90</RefSource><PMID Version="1">17065230</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Elife. 2015 Dec 24;4:e09268</RefSource><PMID Version="1">26705333</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Cell Biol. 1994 Dec;14(12):8219-28</RefSource><PMID Version="1">7969159</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 1997 Oct;7(10):986-95</RefSource><PMID Version="1">9331369</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nat Biotechnol. 2015 Feb;33(2):155-60</RefSource><PMID Version="1">25599176</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Cell Biol. 2000 Sep;20(17):6287-99</RefSource><PMID Version="1">10938105</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Biol. 2014;15(12):550</RefSource><PMID Version="1">25516281</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D017398" MajorTopicYN="N">Alternative Splicing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002453" MajorTopicYN="N">Cell Cycle</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002454" MajorTopicYN="N">Cell Differentiation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005091" MajorTopicYN="N">Exons</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="Y">Gene Expression Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007438" MajorTopicYN="Y">Introns</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059372" MajorTopicYN="N">Nucleotide Motifs</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012326" MajorTopicYN="Y">RNA Splicing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016601" MajorTopicYN="N">RNA-Binding Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Gene regulation</Keyword><Keyword MajorTopicYN="N">Intron retention</Keyword><Keyword MajorTopicYN="N">mRNA splicing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>12</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>02</Month><Day>27</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>3</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>7</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28298237</ArticleId><ArticleId IdType="doi">10.1186/s13059-017-1184-4</ArticleId><ArticleId IdType="pii">10.1186/s13059-017-1184-4</ArticleId><ArticleId IdType="pmc">PMC5353968</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>Espagne</li><li>France</li></country><region><li>Catalogne</li><li>Île-de-France</li></region><settlement><li>Barcelone</li><li>Paris</li></settlement></list><tree><country name="Australie"><noRegion><name sortKey="Middleton, Robert" sort="Middleton, Robert" uniqKey="Middleton R" first="Robert" last="Middleton">Robert Middleton</name></noRegion><name sortKey="Au, Amy" sort="Au, Amy" uniqKey="Au A" first="Amy" last="Au">Amy Au</name><name sortKey="Gao, Dadi" sort="Gao, Dadi" uniqKey="Gao D" first="Dadi" last="Gao">Dadi Gao</name><name sortKey="Rasko, John E J" sort="Rasko, John E J" uniqKey="Rasko J" first="John E J" last="Rasko">John E J. Rasko</name><name sortKey="Ritchie, William" sort="Ritchie, William" uniqKey="Ritchie W" first="William" last="Ritchie">William Ritchie</name><name sortKey="Wong, Justin J L" sort="Wong, Justin J L" uniqKey="Wong J" first="Justin J-L" last="Wong">Justin J-L Wong</name></country><country name="France"><noRegion><name sortKey="Thomas, Aubin" sort="Thomas, Aubin" uniqKey="Thomas A" first="Aubin" last="Thomas">Aubin Thomas</name></noRegion><name sortKey="Bomane, Alexandra" sort="Bomane, Alexandra" uniqKey="Bomane A" first="Alexandra" last="Bomane">Alexandra Bomane</name><name sortKey="Cosson, Bertrand" sort="Cosson, Bertrand" uniqKey="Cosson B" first="Bertrand" last="Cosson">Bertrand Cosson</name></country><country name="Espagne"><region name="Catalogne"><name sortKey="Singh, Babita" sort="Singh, Babita" uniqKey="Singh B" first="Babita" last="Singh">Babita Singh</name></region><name sortKey="Eyras, Eduardo" sort="Eyras, Eduardo" uniqKey="Eyras E" first="Eduardo" last="Eyras">Eduardo Eyras</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Asie/explor/AustralieFrV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000A52 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 000A52 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Asie
|area= AustralieFrV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:28298237
|texte= IRFinder: assessing the impact of intron retention on mammalian gene expression.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:28298237" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a AustralieFrV1
| This area was generated with Dilib version V0.6.33. |  |