Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
Identifieur interne : 001842 ( Main/Exploration ); précédent : 001841; suivant : 001843Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
Auteurs : Marcela Karey Tello-Ruiz [États-Unis] ; Joshua Stein [États-Unis] ; Sharon Wei [États-Unis] ; Ken Youens-Clark [États-Unis] ; Pankaj Jaiswal [États-Unis] ; Doreen Ware [États-Unis]Source :
- Methods in molecular biology (Clifton, N.J.) [ 1940-6029 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Plantes.
- métabolisme : Plantes.
- méthodes : Biologie informatique.
- Génome végétal, Logiciel, Navigateur, Transduction du signal, Voies et réseaux métaboliques.
English descriptors
- KwdEn :
- MESH :
- genetics : Plants.
- metabolism : Plants.
- methods : Computational Biology.
- Genome, Plant, Metabolic Networks and Pathways, Signal Transduction, Software, Web Browser.
Abstract
Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.Moreover, this is the first publication describing Gramene's new web interface-intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations.
DOI: 10.1007/978-1-4939-3167-5_7
PubMed: 26519404
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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type="university">Université Cornell</orgName><placeName><settlement type="city">Ithaca (New York)</settlement><region type="state">État de New York</region></placeName></affiliation></author></analytic><series><title level="j">Methods in molecular biology (Clifton, N.J.)</title><idno type="eISSN">1940-6029</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (methods)</term><term>Genome, Plant (MeSH)</term><term>Metabolic Networks and Pathways (MeSH)</term><term>Plants (genetics)</term><term>Plants (metabolism)</term><term>Signal Transduction (MeSH)</term><term>Software (MeSH)</term><term>Web Browser (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (méthodes)</term><term>Génome végétal (MeSH)</term><term>Logiciel (MeSH)</term><term>Navigateur (MeSH)</term><term>Plantes (génétique)</term><term>Plantes (métabolisme)</term><term>Transduction du signal (MeSH)</term><term>Voies et réseaux métaboliques (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Plantes</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Plantes</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Plant</term><term>Metabolic Networks and Pathways</term><term>Signal Transduction</term><term>Software</term><term>Web Browser</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génome végétal</term><term>Logiciel</term><term>Navigateur</term><term>Transduction du signal</term><term>Voies et réseaux métaboliques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.Moreover, this is the first publication describing Gramene's new web interface-intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26519404</PMID><DateCompleted><Year>2016</Year><Month>05</Month><Day>24</Day></DateCompleted><DateRevised><Year>2015</Year><Month>10</Month><Day>31</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1940-6029</ISSN><JournalIssue CitedMedium="Internet"><Volume>1374</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Methods in molecular biology (Clifton, N.J.)</Title><ISOAbbreviation>Methods Mol Biol</ISOAbbreviation></Journal><ArticleTitle>Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.</ArticleTitle><Pagination><MedlinePgn>141-63</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/978-1-4939-3167-5_7</ELocationID><Abstract><AbstractText>Gramene is an integrated informatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for economically important and research model crops, including wheat, potato, tomato, banana, grape, poplar, and Chlamydomonas. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) view a phylogenetic tree for a family of transcription factors, (2) explore genetic variation in the orthologues of a gene with a known trait association, and (3) upload, visualize, and privately share end user data into a new genome browser track.Moreover, this is the first publication describing Gramene's new web interface-intended to provide a simplified portal to the most complete and up-to-date set of plant genome and pathway annotations. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tello-Ruiz</LastName><ForeName>Marcela Karey</ForeName><Initials>MK</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stein</LastName><ForeName>Joshua</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Sharon</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Youens-Clark</LastName><ForeName>Ken</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jaiswal</LastName><ForeName>Pankaj</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ware</LastName><ForeName>Doreen</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY, 11724, USA. ware@cshl.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>USDA-ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, 14853, USA. ware@cshl.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods Mol Biol</MedlineTA><NlmUniqueID>9214969</NlmUniqueID><ISSNLinking>1064-3745</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053858" MajorTopicYN="N">Metabolic Networks and Pathways</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D064878" MajorTopicYN="N">Web Browser</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Comparative genomic s</Keyword><Keyword MajorTopicYN="N">Gene homology</Keyword><Keyword MajorTopicYN="N">Genetic variation</Keyword><Keyword MajorTopicYN="N">Phylogenetics</Keyword><Keyword MajorTopicYN="N">Plant genome</Keyword><Keyword MajorTopicYN="N">Plant pathway s</Keyword><Keyword MajorTopicYN="N">Reference genome s</Keyword><Keyword MajorTopicYN="N">Structural variation</Keyword><Keyword MajorTopicYN="N">Synteny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>5</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26519404</ArticleId><ArticleId IdType="doi">10.1007/978-1-4939-3167-5_7</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>État de New York</li></region><settlement><li>Ithaca (New York)</li></settlement><orgName><li>Université Cornell</li></orgName></list><tree><country name="États-Unis"><noRegion><name sortKey="Tello Ruiz, Marcela Karey" sort="Tello Ruiz, Marcela Karey" uniqKey="Tello Ruiz M" first="Marcela Karey" last="Tello-Ruiz">Marcela Karey Tello-Ruiz</name></noRegion><name sortKey="Jaiswal, Pankaj" sort="Jaiswal, Pankaj" uniqKey="Jaiswal P" first="Pankaj" last="Jaiswal">Pankaj Jaiswal</name><name sortKey="Stein, Joshua" sort="Stein, Joshua" uniqKey="Stein J" first="Joshua" last="Stein">Joshua Stein</name><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><name sortKey="Ware, Doreen" sort="Ware, Doreen" uniqKey="Ware D" first="Doreen" last="Ware">Doreen Ware</name><name sortKey="Wei, Sharon" sort="Wei, Sharon" uniqKey="Wei S" first="Sharon" last="Wei">Sharon Wei</name><name sortKey="Youens Clark, Ken" sort="Youens Clark, Ken" uniqKey="Youens Clark K" first="Ken" last="Youens-Clark">Ken Youens-Clark</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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