Modular gene expression in Poplar: a multilayer network approach.
Identifieur interne : 003562 ( Main/Exploration ); précédent : 003561; suivant : 003563Modular gene expression in Poplar: a multilayer network approach.
Auteurs : Andreas Grönlund [Suède] ; Rishikesh P. Bhalerao [Suède] ; Jan Karlsson [Suède]Source :
- The New phytologist [ 1469-8137 ] ; 2009.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Analyse de profil d'expression de gènes (MeSH), Biologie informatique (MeSH), Cartographie d'interactions entre protéines (MeSH), Gènes dupliqués (MeSH), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Séquençage par oligonucléotides en batterie (méthodes), Transduction du signal (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
Abstract
By applying a multilayer network approach to an extensive set of Poplar microarray data, a genome-wide coexpression network has been detected and explored. Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack-knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs. The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene-to-gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over- and/or under-expression patterns at the modular scale. It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be 'weak' because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random 'null networks', tuning to maximize the information obtainable.
DOI: 10.1111/j.1469-8137.2008.02668.x
PubMed: 19121030
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack-knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs. The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene-to-gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over- and/or under-expression patterns at the modular scale. It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be 'weak' because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random 'null networks', tuning to maximize the information obtainable.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19121030</PMID><DateCompleted><Year>2009</Year><Month>02</Month><Day>10</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>181</Volume><Issue>2</Issue><PubDate><Year>2009</Year><Month>Jan</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Modular gene expression in Poplar: a multilayer network approach.</ArticleTitle><Pagination><MedlinePgn>315-322</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1469-8137.2008.02668.x</ELocationID><Abstract><AbstractText>By applying a multilayer network approach to an extensive set of Poplar microarray data, a genome-wide coexpression network has been detected and explored. Multilayer networks were generated from minimum spanning trees (MSTs) using Kruskal's algorithm from random jack-knife resamplings of half of the full data set. The final network is obtained from the union of all the generated MSTs. The gene expression correlations display a highly clustered topology, which is more pronounced when introducing links appearing in relatively few of the generated MSTs. The network also reveals a modular architecture, reflecting functional groups with relatively frequent gene-to-gene communication. Furthermore, the observed modular structure overlaps with different gene activities in different tissues, and closely related tissues show similar over- and/or under-expression patterns at the modular scale. It is shown that including links that appear in a few of the generated MSTs increases the information quality of the network. In other words, a link may be 'weak' because it reflects rare signaling events rather than merely a signal weakened by noise. The method allows, from comparisons of random 'null networks', tuning to maximize the information obtainable.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Grönlund</LastName><ForeName>Andreas</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bhalerao</LastName><ForeName>Rishikesh P</ForeName><Initials>RP</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Karlsson</LastName><ForeName>Jan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.</Affiliation></AffiliationInfo></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>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020131" MajorTopicYN="N">Genes, Duplicate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025941" MajorTopicYN="N">Protein Interaction Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>1</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>1</Month><Day>6</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>2</Month><Day>12</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19121030</ArticleId><ArticleId IdType="doi">10.1111/j.1469-8137.2008.02668.x</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Suède</li></country></list><tree><country name="Suède"><noRegion><name sortKey="Gronlund, Andreas" sort="Gronlund, Andreas" uniqKey="Gronlund A" first="Andreas" last="Grönlund">Andreas Grönlund</name></noRegion><name sortKey="Bhalerao, Rishikesh P" sort="Bhalerao, Rishikesh P" uniqKey="Bhalerao R" first="Rishikesh P" last="Bhalerao">Rishikesh P. 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