Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen.
Identifieur interne : 003584 ( Main/Exploration ); précédent : 003583; suivant : 003585Integrated analysis of transcript, protein and metabolite data to study lignin biosynthesis in hybrid aspen.
Auteurs : Max Bylesjö [Suède] ; Robert Nilsson ; Vaibhav Srivastava ; Andreas Grönlund ; Annika I. Johansson ; Steffan Jansson ; Jan Karlsson ; Thomas Moritz ; Gunnar Wingsle ; Johan TryggSource :
- Journal of proteome research [ 1535-3893 ] ; 2009.
Descripteurs français
- KwdFr :
- ADN complémentaire (métabolisme), Arbres (métabolisme), Biologie informatique (méthodes), Chimère (métabolisme), Gènes de plante (MeSH), Génotype (MeSH), Lignine (biosynthèse), Lignine (composition chimique), Modèles théoriques (MeSH), Peptides (composition chimique), Populus (MeSH), Protéome (MeSH), Protéomique (méthodes), Spectrométrie de masse (méthodes), Séquençage par oligonucléotides en batterie (MeSH), Transcription génétique (MeSH).
- MESH :
- biosynthèse : Lignine.
- composition chimique : Lignine, Peptides.
- métabolisme : ADN complémentaire, Arbres, Chimère.
- méthodes : Biologie informatique, Protéomique, Spectrométrie de masse.
- Gènes de plante, Génotype, Modèles théoriques, Populus, Protéome, Séquençage par oligonucléotides en batterie, Transcription génétique.
English descriptors
- KwdEn :
- Chimera (metabolism), Computational Biology (methods), DNA, Complementary (metabolism), Genes, Plant (MeSH), Genotype (MeSH), Lignin (biosynthesis), Lignin (chemistry), Mass Spectrometry (methods), Models, Theoretical (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Peptides (chemistry), Populus (MeSH), Proteome (MeSH), Proteomics (methods), Transcription, Genetic (MeSH), Trees (metabolism).
- MESH :
- chemical , biosynthesis : Lignin.
- chemical , chemistry : Lignin, Peptides.
- chemical , metabolism : DNA, Complementary.
- metabolism : Chimera, Trees.
- methods : Computational Biology, Mass Spectrometry, Proteomics.
- Genes, Plant, Genotype, Models, Theoretical, Oligonucleotide Array Sequence Analysis, Populus, Proteome, Transcription, Genetic.
Abstract
Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.
DOI: 10.1021/pr800298s
PubMed: 19053836
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Johansson</name></author><author><name sortKey="Jansson, Steffan" sort="Jansson, Steffan" uniqKey="Jansson S" first="Steffan" last="Jansson">Steffan Jansson</name></author><author><name sortKey="Karlsson, Jan" sort="Karlsson, Jan" uniqKey="Karlsson J" first="Jan" last="Karlsson">Jan Karlsson</name></author><author><name sortKey="Moritz, Thomas" sort="Moritz, Thomas" uniqKey="Moritz T" first="Thomas" last="Moritz">Thomas Moritz</name></author><author><name sortKey="Wingsle, Gunnar" sort="Wingsle, Gunnar" uniqKey="Wingsle G" first="Gunnar" last="Wingsle">Gunnar Wingsle</name></author><author><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name></author></analytic><series><title level="j">Journal of proteome research</title><idno type="ISSN">1535-3893</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chimera (metabolism)</term><term>Computational Biology (methods)</term><term>DNA, Complementary (metabolism)</term><term>Genes, Plant (MeSH)</term><term>Genotype (MeSH)</term><term>Lignin (biosynthesis)</term><term>Lignin (chemistry)</term><term>Mass Spectrometry (methods)</term><term>Models, Theoretical (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Peptides (chemistry)</term><term>Populus (MeSH)</term><term>Proteome (MeSH)</term><term>Proteomics (methods)</term><term>Transcription, Genetic (MeSH)</term><term>Trees (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (métabolisme)</term><term>Arbres (métabolisme)</term><term>Biologie informatique (méthodes)</term><term>Chimère (métabolisme)</term><term>Gènes de plante (MeSH)</term><term>Génotype (MeSH)</term><term>Lignine (biosynthèse)</term><term>Lignine (composition chimique)</term><term>Modèles théoriques (MeSH)</term><term>Peptides (composition chimique)</term><term>Populus (MeSH)</term><term>Protéome (MeSH)</term><term>Protéomique (méthodes)</term><term>Spectrométrie de masse (méthodes)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Transcription génétique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Lignin</term><term>Peptides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Complementary</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Lignine</term><term>Peptides</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Chimera</term><term>Trees</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Mass Spectrometry</term><term>Proteomics</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN complémentaire</term><term>Arbres</term><term>Chimère</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term><term>Protéomique</term><term>Spectrométrie de masse</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genes, Plant</term><term>Genotype</term><term>Models, Theoretical</term><term>Oligonucleotide Array Sequence Analysis</term><term>Populus</term><term>Proteome</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Gènes de plante</term><term>Génotype</term><term>Modèles théoriques</term><term>Populus</term><term>Protéome</term><term>Séquençage par oligonucléotides en batterie</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber, energy and wood products. 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We are now ready to make the transition from identifying candidate genes, controlling important biological processes, to discovering the detailed molecular function of these genes on a broader, more holistic, systems biology level. In this paper, a strategy is outlined for informative data generation and integrated modeling of systematic changes in transcript, protein and metabolite profiles measured from hybrid aspen samples. The aim is to study characteristics of common changes in relation to genotype-specific perturbations affecting the lignin biosynthesis and growth. We show that a considerable part of the systematic effects in the system can be tracked across all platforms and that the approach has a high potential value in functional characterization of candidate genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bylesjö</LastName><ForeName>Max</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nilsson</LastName><ForeName>Robert</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Srivastava</LastName><ForeName>Vaibhav</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Grönlund</LastName><ForeName>Andreas</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Johansson</LastName><ForeName>Annika I</ForeName><Initials>AI</Initials></Author><Author ValidYN="Y"><LastName>Jansson</LastName><ForeName>Steffan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Karlsson</LastName><ForeName>Jan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Moritz</LastName><ForeName>Thomas</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Wingsle</LastName><ForeName>Gunnar</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Trygg</LastName><ForeName>Johan</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Proteome 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PubStatus="pubmed"><Year>2008</Year><Month>12</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>2</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>12</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19053836</ArticleId><ArticleId IdType="doi">10.1021/pr800298s</ArticleId><ArticleId IdType="pii">10.1021/pr800298s</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Suède</li></country></list><tree><noCountry><name sortKey="Gronlund, Andreas" sort="Gronlund, Andreas" uniqKey="Gronlund A" first="Andreas" last="Grönlund">Andreas Grönlund</name><name sortKey="Jansson, Steffan" sort="Jansson, Steffan" uniqKey="Jansson S" first="Steffan" last="Jansson">Steffan Jansson</name><name sortKey="Johansson, Annika I" sort="Johansson, Annika I" uniqKey="Johansson A" first="Annika I" last="Johansson">Annika I. Johansson</name><name sortKey="Karlsson, Jan" sort="Karlsson, Jan" uniqKey="Karlsson J" first="Jan" last="Karlsson">Jan Karlsson</name><name sortKey="Moritz, Thomas" sort="Moritz, Thomas" uniqKey="Moritz T" first="Thomas" last="Moritz">Thomas Moritz</name><name sortKey="Nilsson, Robert" sort="Nilsson, Robert" uniqKey="Nilsson R" first="Robert" last="Nilsson">Robert Nilsson</name><name sortKey="Srivastava, Vaibhav" sort="Srivastava, Vaibhav" uniqKey="Srivastava V" first="Vaibhav" last="Srivastava">Vaibhav Srivastava</name><name sortKey="Trygg, Johan" sort="Trygg, Johan" uniqKey="Trygg J" first="Johan" last="Trygg">Johan Trygg</name><name sortKey="Wingsle, Gunnar" sort="Wingsle, Gunnar" uniqKey="Wingsle G" first="Gunnar" last="Wingsle">Gunnar Wingsle</name></noCountry><country name="Suède"><noRegion><name sortKey="Bylesjo, Max" sort="Bylesjo, Max" uniqKey="Bylesjo M" first="Max" last="Bylesjö">Max Bylesjö</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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