The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Identifieur interne : 003A63 ( Main/Exploration ); précédent : 003A62; suivant : 003A64The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Auteurs : T C Mockler [États-Unis] ; T P Michael ; H D Priest ; R. Shen ; C M Sullivan ; S A Givan ; C. Mcentee ; S A Kay ; J. ChorySource :
- Cold Spring Harbor symposia on quantitative biology [ 0091-7451 ] ; 2007.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Algorithmes (MeSH), Analyse de profil d'expression de gènes (statistiques et données numériques), Arabidopsis (génétique), Arabidopsis (physiologie), Bases de données génétiques (MeSH), Gènes de plante (MeSH), Logiciel (MeSH), Modèles génétiques (MeSH), Oryza (génétique), Oryza (physiologie), Phénomènes physiologiques des plantes (MeSH), Plantes (génétique), Populus (génétique), Populus (physiologie), Reconnaissance automatique des formes (MeSH), Rythme circadien (génétique), Rythme circadien (physiologie), Régions promotrices (génétique) (MeSH), Séquençage par oligonucléotides en batterie (statistiques et données numériques), Éléments de régulation transcriptionnelle (MeSH).
- MESH :
- génétique : ADN des plantes, Arabidopsis, Oryza, Plantes, Populus, Rythme circadien.
- physiologie : Arabidopsis, Oryza, Populus, Rythme circadien.
- statistiques et données numériques : Analyse de profil d'expression de gènes, Séquençage par oligonucléotides en batterie.
- Algorithmes, Bases de données génétiques, Gènes de plante, Logiciel, Modèles génétiques, Phénomènes physiologiques des plantes, Reconnaissance automatique des formes, Régions promotrices (génétique), Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- Algorithms (MeSH), Arabidopsis (genetics), Arabidopsis (physiology), Circadian Rhythm (genetics), Circadian Rhythm (physiology), DNA, Plant (genetics), Databases, Genetic (MeSH), Gene Expression Profiling (statistics & numerical data), Genes, Plant (MeSH), Models, Genetic (MeSH), Oligonucleotide Array Sequence Analysis (statistics & numerical data), Oryza (genetics), Oryza (physiology), Pattern Recognition, Automated (MeSH), Plant Physiological Phenomena (MeSH), Plants (genetics), Populus (genetics), Populus (physiology), Promoter Regions, Genetic (MeSH), Regulatory Elements, Transcriptional (MeSH), Software (MeSH).
- MESH :
- chemical , genetics : DNA, Plant.
- genetics : Arabidopsis, Circadian Rhythm, Oryza, Plants, Populus.
- physiology : Arabidopsis, Circadian Rhythm, Oryza, Populus.
- statistics & numerical data : Gene Expression Profiling, Oligonucleotide Array Sequence Analysis.
- Algorithms, Databases, Genetic, Genes, Plant, Models, Genetic, Pattern Recognition, Automated, Plant Physiological Phenomena, Promoter Regions, Genetic, Regulatory Elements, Transcriptional, Software.
Abstract
The DIURNAL project ( http://diurnal.cgrb.oregonstate.edu/ ) provides a graphical interface for mining and viewing diurnal and circadian microarray data for Arabidopsis thaliana, poplar, and rice. The database is searchable and provides access to several user-friendly Web-based data-mining tools with easy-to-understand output. The associated tools include HAYSTACK ( http://haystack.cgrb.oregonstate.edu/ ) and ELEMENT ( http://element.cgrb.oregonstate.edu/ ). HAYSTACK is a model-based pattern-matching algorithm for identifying genes that are coexpressed and potentially coregulated. HAYSTACK can be used to analyze virtually any large-scale microarray data set and provides an alternative method for clustering microarray data from any experimental system by grouping together genes whose expression patterns match the same or similar user-defined patterns. ELEMENT is a Web-based program for identifying potential cis-regulatory elements in the promoters of coregulated genes in Arabidopsis, poplar, and rice. Together, DIURNAL, HAYSTACK, and ELEMENT can be used to facilitate cross-species comparisons among the plant species supported and to accelerate functional genomics efforts in the laboratory.
DOI: 10.1101/sqb.2007.72.006
PubMed: 18419293
Affiliations:
Links toward previous steps (curation, corpus...)
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Chory</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:18419293</idno><idno type="pmid">18419293</idno><idno type="doi">10.1101/sqb.2007.72.006</idno><idno type="wicri:Area/Main/Corpus">003917</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003917</idno><idno type="wicri:Area/Main/Curation">003917</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003917</idno><idno type="wicri:Area/Main/Exploration">003917</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.</title><author><name sortKey="Mockler, T C" sort="Mockler, T C" uniqKey="Mockler T" first="T C" last="Mockler">T C Mockler</name><affiliation wicri:level="1"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331</wicri:regionArea><wicri:noRegion>Oregon 97331</wicri:noRegion></affiliation></author><author><name sortKey="Michael, T P" sort="Michael, T P" uniqKey="Michael T" first="T P" last="Michael">T P Michael</name></author><author><name sortKey="Priest, H D" sort="Priest, H D" uniqKey="Priest H" first="H D" last="Priest">H D Priest</name></author><author><name sortKey="Shen, R" sort="Shen, R" uniqKey="Shen R" first="R" last="Shen">R. Shen</name></author><author><name sortKey="Sullivan, C M" sort="Sullivan, C M" uniqKey="Sullivan C" first="C M" last="Sullivan">C M Sullivan</name></author><author><name sortKey="Givan, S A" sort="Givan, S A" uniqKey="Givan S" first="S A" last="Givan">S A Givan</name></author><author><name sortKey="Mcentee, C" sort="Mcentee, C" uniqKey="Mcentee C" first="C" last="Mcentee">C. Mcentee</name></author><author><name sortKey="Kay, S A" sort="Kay, S A" uniqKey="Kay S" first="S A" last="Kay">S A Kay</name></author><author><name sortKey="Chory, J" sort="Chory, J" uniqKey="Chory J" first="J" last="Chory">J. Chory</name></author></analytic><series><title level="j">Cold Spring Harbor symposia on quantitative biology</title><idno type="ISSN">0091-7451</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Arabidopsis (genetics)</term><term>Arabidopsis (physiology)</term><term>Circadian Rhythm (genetics)</term><term>Circadian Rhythm (physiology)</term><term>DNA, Plant (genetics)</term><term>Databases, Genetic (MeSH)</term><term>Gene Expression Profiling (statistics & numerical data)</term><term>Genes, Plant (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (statistics & numerical data)</term><term>Oryza (genetics)</term><term>Oryza (physiology)</term><term>Pattern Recognition, Automated (MeSH)</term><term>Plant Physiological Phenomena (MeSH)</term><term>Plants (genetics)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Promoter Regions, Genetic (MeSH)</term><term>Regulatory Elements, Transcriptional (MeSH)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Algorithmes (MeSH)</term><term>Analyse de profil d'expression de gènes (statistiques et données numériques)</term><term>Arabidopsis (génétique)</term><term>Arabidopsis (physiologie)</term><term>Bases de données génétiques (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Logiciel (MeSH)</term><term>Modèles génétiques (MeSH)</term><term>Oryza (génétique)</term><term>Oryza (physiologie)</term><term>Phénomènes physiologiques des plantes (MeSH)</term><term>Plantes (génétique)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Reconnaissance automatique des formes (MeSH)</term><term>Rythme circadien (génétique)</term><term>Rythme circadien (physiologie)</term><term>Régions promotrices (génétique) (MeSH)</term><term>Séquençage par oligonucléotides en batterie (statistiques et données numériques)</term><term>Éléments de régulation transcriptionnelle (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Circadian Rhythm</term><term>Oryza</term><term>Plants</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Arabidopsis</term><term>Oryza</term><term>Plantes</term><term>Populus</term><term>Rythme circadien</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Arabidopsis</term><term>Oryza</term><term>Populus</term><term>Rythme circadien</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Arabidopsis</term><term>Circadian Rhythm</term><term>Oryza</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Gene Expression Profiling</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="statistiques et données numériques" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Databases, Genetic</term><term>Genes, Plant</term><term>Models, Genetic</term><term>Pattern Recognition, Automated</term><term>Plant Physiological Phenomena</term><term>Promoter Regions, Genetic</term><term>Regulatory Elements, Transcriptional</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Bases de données génétiques</term><term>Gènes de plante</term><term>Logiciel</term><term>Modèles génétiques</term><term>Phénomènes physiologiques des plantes</term><term>Reconnaissance automatique des formes</term><term>Régions promotrices (génétique)</term><term>Éléments de régulation transcriptionnelle</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The DIURNAL project ( http://diurnal.cgrb.oregonstate.edu/ ) provides a graphical interface for mining and viewing diurnal and circadian microarray data for Arabidopsis thaliana, poplar, and rice. The database is searchable and provides access to several user-friendly Web-based data-mining tools with easy-to-understand output. The associated tools include HAYSTACK ( http://haystack.cgrb.oregonstate.edu/ ) and ELEMENT ( http://element.cgrb.oregonstate.edu/ ). HAYSTACK is a model-based pattern-matching algorithm for identifying genes that are coexpressed and potentially coregulated. HAYSTACK can be used to analyze virtually any large-scale microarray data set and provides an alternative method for clustering microarray data from any experimental system by grouping together genes whose expression patterns match the same or similar user-defined patterns. ELEMENT is a Web-based program for identifying potential cis-regulatory elements in the promoters of coregulated genes in Arabidopsis, poplar, and rice. Together, DIURNAL, HAYSTACK, and ELEMENT can be used to facilitate cross-species comparisons among the plant species supported and to accelerate functional genomics efforts in the laboratory.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18419293</PMID><DateCompleted><Year>2008</Year><Month>08</Month><Day>01</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>19</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0091-7451</ISSN><JournalIssue CitedMedium="Print"><Volume>72</Volume><PubDate><Year>2007</Year></PubDate></JournalIssue><Title>Cold Spring Harbor symposia on quantitative biology</Title><ISOAbbreviation>Cold Spring Harb Symp Quant Biol</ISOAbbreviation></Journal><ArticleTitle>The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.</ArticleTitle><Pagination><MedlinePgn>353-63</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/sqb.2007.72.006</ELocationID><Abstract><AbstractText>The DIURNAL project ( http://diurnal.cgrb.oregonstate.edu/ ) provides a graphical interface for mining and viewing diurnal and circadian microarray data for Arabidopsis thaliana, poplar, and rice. The database is searchable and provides access to several user-friendly Web-based data-mining tools with easy-to-understand output. The associated tools include HAYSTACK ( http://haystack.cgrb.oregonstate.edu/ ) and ELEMENT ( http://element.cgrb.oregonstate.edu/ ). HAYSTACK is a model-based pattern-matching algorithm for identifying genes that are coexpressed and potentially coregulated. HAYSTACK can be used to analyze virtually any large-scale microarray data set and provides an alternative method for clustering microarray data from any experimental system by grouping together genes whose expression patterns match the same or similar user-defined patterns. ELEMENT is a Web-based program for identifying potential cis-regulatory elements in the promoters of coregulated genes in Arabidopsis, poplar, and rice. Together, DIURNAL, HAYSTACK, and ELEMENT can be used to facilitate cross-species comparisons among the plant species supported and to accelerate functional genomics efforts in the laboratory.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mockler</LastName><ForeName>T C</ForeName><Initials>TC</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Michael</LastName><ForeName>T P</ForeName><Initials>TP</Initials></Author><Author ValidYN="Y"><LastName>Priest</LastName><ForeName>H D</ForeName><Initials>HD</Initials></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Sullivan</LastName><ForeName>C M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Givan</LastName><ForeName>S A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>McEntee</LastName><ForeName>C</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Kay</LastName><ForeName>S A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>Chory</LastName><ForeName>J</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01 GM052413</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM62932</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM56006</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM67837</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>GM52413</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><Agency>Howard Hughes Medical Institute</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Cold Spring Harb Symp Quant Biol</MedlineTA><NlmUniqueID>1256107</NlmUniqueID><ISSNLinking>0091-7451</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002940" MajorTopicYN="N">Circadian Rhythm</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000706" MajorTopicYN="N">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000706" MajorTopicYN="N">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010363" MajorTopicYN="N">Pattern Recognition, Automated</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018521" MajorTopicYN="N">Plant Physiological Phenomena</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D050436" MajorTopicYN="N">Regulatory Elements, Transcriptional</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="N">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>4</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>8</Month><Day>2</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>4</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18419293</ArticleId><ArticleId IdType="doi">10.1101/sqb.2007.72.006</ArticleId><ArticleId IdType="pii">10.1101/sqb.2007.72.006</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Chory, J" sort="Chory, J" uniqKey="Chory J" first="J" last="Chory">J. Chory</name><name sortKey="Givan, S A" sort="Givan, S A" uniqKey="Givan S" first="S A" last="Givan">S A Givan</name><name sortKey="Kay, S A" sort="Kay, S A" uniqKey="Kay S" first="S A" last="Kay">S A Kay</name><name sortKey="Mcentee, C" sort="Mcentee, C" uniqKey="Mcentee C" first="C" last="Mcentee">C. Mcentee</name><name sortKey="Michael, T P" sort="Michael, T P" uniqKey="Michael T" first="T P" last="Michael">T P Michael</name><name sortKey="Priest, H D" sort="Priest, H D" uniqKey="Priest H" first="H D" last="Priest">H D Priest</name><name sortKey="Shen, R" sort="Shen, R" uniqKey="Shen R" first="R" last="Shen">R. Shen</name><name sortKey="Sullivan, C M" sort="Sullivan, C M" uniqKey="Sullivan C" first="C M" last="Sullivan">C M Sullivan</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Mockler, T C" sort="Mockler, T C" uniqKey="Mockler T" first="T C" last="Mockler">T C Mockler</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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