A program toolkit for the analysis of regulatory regions of genes.
Identifieur interne : 002234 ( PubMed/Curation ); précédent : 002233; suivant : 002235A 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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: Pour aller vers cette notice dans l'étape Curation :002234
Links to Exploration step
pubmed:16888356Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A program toolkit for the analysis of regulatory regions of genes.</title>
<author><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Purdue University, West Lafayette, IN</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name>
</author>
<author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2006">2006</date>
<idno type="RBID">pubmed:16888356</idno>
<idno type="pmid">16888356</idno>
<idno type="doi">10.1385/1-59745-097-9:135</idno>
<idno type="wicri:Area/PubMed/Corpus">002234</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002234</idno>
<idno type="wicri:Area/PubMed/Curation">002234</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002234</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">A program toolkit for the analysis of regulatory regions of genes.</title>
<author><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Purdue University, West Lafayette, IN</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name>
</author>
<author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
</author>
</analytic>
<series><title level="j">Methods in molecular biology (Clifton, N.J.)</title>
<idno type="ISSN">1064-3745</idno>
<imprint><date when="2006" type="published">2006</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites (genetics)</term>
<term>DNA (genetics)</term>
<term>DNA (metabolism)</term>
<term>Databases, Nucleic Acid</term>
<term>Genes, Regulator</term>
<term>Genome, Human</term>
<term>Genomics (statistics & numerical data)</term>
<term>Humans</term>
<term>Software</term>
<term>Systems Biology</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term>
<term>ADN (métabolisme)</term>
<term>Bases de données d'acides nucléiques</term>
<term>Biologie des systèmes</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Gènes régulateurs</term>
<term>Génome humain</term>
<term>Génomique ()</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Sites de fixation (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Binding Sites</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term>
<term>Sites de fixation</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term>
<term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" qualifier="statistics & numerical data" xml:lang="en"><term>Genomics</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term>
<term>Genes, Regulator</term>
<term>Genome, Human</term>
<term>Humans</term>
<term>Software</term>
<term>Systems Biology</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term>
<term>Biologie des systèmes</term>
<term>Gènes régulateurs</term>
<term>Génome humain</term>
<term>Génomique</term>
<term>Humains</term>
<term>Logiciel</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">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.</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>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002234 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd -nk 002234 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Curation |type= RBID |clé= pubmed:16888356 |texte= A program toolkit for the analysis of regulatory regions of genes. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Curation/RBID.i -Sk "pubmed:16888356" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Curation/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |