A program toolkit for the analysis of regulatory regions of genes.
Identifieur interne : 000456 ( Ncbi/Merge ); précédent : 000455; suivant : 000457A program toolkit for the analysis of regulatory regions of genes.
Auteurs : Phillip Wyss [États-Unis] ; Sheryl A. Lazarus ; Minou BinaSource :
- Methods in molecular biology (Clifton, N.J.) [ 1064-3745 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN, Sites de fixation.
- métabolisme : ADN, Facteurs de transcription.
- Bases de données d'acides nucléiques, Biologie des systèmes, Gènes régulateurs, Génome humain, Génomique, Humains, Logiciel.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- genetics : Binding Sites.
- chemical , metabolism : DNA, Transcription Factors.
- statistics & numerical data : Genomics.
- Databases, Nucleic Acid, Genes, Regulator, Genome, Human, Humans, Software, Systems Biology.
Abstract
A major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. Even though a variety of sequences have been shown to interact with the transcription factors that bind DNA, extensive work is needed to discover and classify regulatory "codes" and to elucidate the role played by the sequence context of genomic DNA in the regulation of genes. Databases of sequence elements extracted from regulatory regions may facilitate this process. This report provides a Toolkit and instructions for creating a database for collecting and analyzing 9-base elements (9-mers) from a large collection of DNA sequences. A reference set consisting of all possible 9-mers is included for extracting potential control elements, irrespective of their orientation and order in DNA.
DOI: 10.1385/1-59745-097-9:135
PubMed: 16888356
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pubmed:16888356Le document en format XML
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Even though a variety of sequences have been shown to interact with the transcription factors that bind DNA, extensive work is needed to discover and classify regulatory "codes" and to elucidate the role played by the sequence context of genomic DNA in the regulation of genes. Databases of sequence elements extracted from regulatory regions may facilitate this process. This report provides a Toolkit and instructions for creating a database for collecting and analyzing 9-base elements (9-mers) from a large collection of DNA sequences. A reference set consisting of all possible 9-mers is included for extracting potential control elements, irrespective of their orientation and order in DNA.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16888356</PMID><DateCompleted><Year>2006</Year><Month>09</Month><Day>28</Day></DateCompleted><DateRevised><Year>2006</Year><Month>08</Month><Day>04</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1064-3745</ISSN><JournalIssue CitedMedium="Print"><Volume>338</Volume><PubDate><Year>2006</Year></PubDate></JournalIssue><Title>Methods in molecular biology (Clifton, N.J.)</Title><ISOAbbreviation>Methods Mol. Biol.</ISOAbbreviation></Journal><ArticleTitle>A program toolkit for the analysis of regulatory regions of genes.</ArticleTitle><Pagination><MedlinePgn>135-52</MedlinePgn></Pagination><Abstract><AbstractText>A major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. Even though a variety of sequences have been shown to interact with the transcription factors that bind DNA, extensive work is needed to discover and classify regulatory "codes" and to elucidate the role played by the sequence context of genomic DNA in the regulation of genes. Databases of sequence elements extracted from regulatory regions may facilitate this process. This report provides a Toolkit and instructions for creating a database for collecting and analyzing 9-base elements (9-mers) from a large collection of DNA sequences. A reference set consisting of all possible 9-mers is included for extracting potential control elements, irrespective of their orientation and order in DNA.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wyss</LastName><ForeName>Phillip</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Purdue University, West Lafayette, IN, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lazarus</LastName><ForeName>Sheryl A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>Bina</LastName><ForeName>Minou</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Methods Mol Biol</MedlineTA><NlmUniqueID>9214969</NlmUniqueID><ISSNLinking>1064-3745</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="Y">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005809" MajorTopicYN="Y">Genes, Regulator</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015894" MajorTopicYN="N">Genome, Human</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000706" MajorTopicYN="N">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D049490" MajorTopicYN="N">Systems Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>8</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>9</Month><Day>29</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>8</Month><Day>5</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16888356</ArticleId><ArticleId IdType="pii">1-59745-097-9:135</ArticleId><ArticleId IdType="doi">10.1385/1-59745-097-9:135</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Indiana</li></region></list><tree><noCountry><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name><name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name></noCountry><country name="États-Unis"><region name="Indiana"><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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