Discovering sequences with potential regulatory characteristics.
Identifieur interne : 001F18 ( PubMed/Checkpoint ); précédent : 001F17; suivant : 001F19Discovering sequences with potential regulatory characteristics.
Auteurs : Minou Bina [États-Unis] ; Phillip Wyss ; Sheryl A. Lazarus ; Syed R. Shah ; Wenhui Ren ; Wojciech Szpankowski ; Gregory E. Crawford ; Sang P. Park ; Xiaohui C. SongSource :
- Genomics [ 1089-8646 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- genetics : Chromosomes, Human, Pair 7, Homeodomain Proteins, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid.
- chemical , metabolism : DNA.
- methods : Computational Biology.
- Binding Sites, Genome, Human, Humans.
Abstract
We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.
DOI: 10.1016/j.ygeno.2008.11.008
PubMed: 19084590
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:19084590Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Discovering sequences with potential regulatory characteristics.</title>
<author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. Bina@Purdue.edu</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Purdue University, West Lafayette, IN 47907</wicri:regionArea>
<placeName><region type="state">Indiana</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
</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="Shah, Syed R" sort="Shah, Syed R" uniqKey="Shah S" first="Syed R" last="Shah">Syed R. Shah</name>
</author>
<author><name sortKey="Ren, Wenhui" sort="Ren, Wenhui" uniqKey="Ren W" first="Wenhui" last="Ren">Wenhui Ren</name>
</author>
<author><name sortKey="Szpankowski, Wojciech" sort="Szpankowski, Wojciech" uniqKey="Szpankowski W" first="Wojciech" last="Szpankowski">Wojciech Szpankowski</name>
</author>
<author><name sortKey="Crawford, Gregory E" sort="Crawford, Gregory E" uniqKey="Crawford G" first="Gregory E" last="Crawford">Gregory E. Crawford</name>
</author>
<author><name sortKey="Park, Sang P" sort="Park, Sang P" uniqKey="Park S" first="Sang P" last="Park">Sang P. Park</name>
</author>
<author><name sortKey="Song, Xiaohui C" sort="Song, Xiaohui C" uniqKey="Song X" first="Xiaohui C" last="Song">Xiaohui C. Song</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2009">2009</date>
<idno type="RBID">pubmed:19084590</idno>
<idno type="pmid">19084590</idno>
<idno type="doi">10.1016/j.ygeno.2008.11.008</idno>
<idno type="wicri:Area/PubMed/Corpus">002055</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002055</idno>
<idno type="wicri:Area/PubMed/Curation">002055</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002055</idno>
<idno type="wicri:Area/PubMed/Checkpoint">001F18</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F18</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Discovering sequences with potential regulatory characteristics.</title>
<author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
<affiliation wicri:level="2"><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. Bina@Purdue.edu</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Chemistry, Purdue University, West Lafayette, IN 47907</wicri:regionArea>
<placeName><region type="state">Indiana</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
</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="Shah, Syed R" sort="Shah, Syed R" uniqKey="Shah S" first="Syed R" last="Shah">Syed R. Shah</name>
</author>
<author><name sortKey="Ren, Wenhui" sort="Ren, Wenhui" uniqKey="Ren W" first="Wenhui" last="Ren">Wenhui Ren</name>
</author>
<author><name sortKey="Szpankowski, Wojciech" sort="Szpankowski, Wojciech" uniqKey="Szpankowski W" first="Wojciech" last="Szpankowski">Wojciech Szpankowski</name>
</author>
<author><name sortKey="Crawford, Gregory E" sort="Crawford, Gregory E" uniqKey="Crawford G" first="Gregory E" last="Crawford">Gregory E. Crawford</name>
</author>
<author><name sortKey="Park, Sang P" sort="Park, Sang P" uniqKey="Park S" first="Sang P" last="Park">Sang P. Park</name>
</author>
<author><name sortKey="Song, Xiaohui C" sort="Song, Xiaohui C" uniqKey="Song X" first="Xiaohui C" last="Song">Xiaohui C. Song</name>
</author>
</analytic>
<series><title level="j">Genomics</title>
<idno type="eISSN">1089-8646</idno>
<imprint><date when="2009" type="published">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term>
<term>Chromosomes, Human, Pair 7 (genetics)</term>
<term>Computational Biology (methods)</term>
<term>DNA (chemistry)</term>
<term>DNA (metabolism)</term>
<term>Genome, Human</term>
<term>Homeodomain Proteins (genetics)</term>
<term>Humans</term>
<term>Promoter Regions, Genetic (genetics)</term>
<term>Regulatory Sequences, Nucleic Acid (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term>
<term>ADN (métabolisme)</term>
<term>Biologie informatique ()</term>
<term>Chromosomes humains de la paire 7 (génétique)</term>
<term>Génome humain</term>
<term>Humains</term>
<term>Protéines à homéodomaine (génétique)</term>
<term>Régions promotrices (génétique) (génétique)</term>
<term>Sites de fixation</term>
<term>Séquences d'acides nucléiques régulatrices (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Human, Pair 7</term>
<term>Homeodomain Proteins</term>
<term>Promoter Regions, Genetic</term>
<term>Regulatory Sequences, Nucleic Acid</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes humains de la paire 7</term>
<term>Protéines à homéodomaine</term>
<term>Régions promotrices (génétique)</term>
<term>Séquences d'acides nucléiques régulatrices</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term>
<term>Genome, Human</term>
<term>Humans</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>ADN</term>
<term>Biologie informatique</term>
<term>Génome humain</term>
<term>Humains</term>
<term>Sites de fixation</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19084590</PMID>
<DateCompleted><Year>2009</Year>
<Month>04</Month>
<Day>15</Day>
</DateCompleted>
<DateRevised><Year>2009</Year>
<Month>03</Month>
<Day>16</Day>
</DateRevised>
<Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1089-8646</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>93</Volume>
<Issue>4</Issue>
<PubDate><Year>2009</Year>
<Month>Apr</Month>
</PubDate>
</JournalIssue>
<Title>Genomics</Title>
<ISOAbbreviation>Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Discovering sequences with potential regulatory characteristics.</ArticleTitle>
<Pagination><MedlinePgn>314-22</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ygeno.2008.11.008</ELocationID>
<Abstract><AbstractText>We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bina</LastName>
<ForeName>Minou</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. Bina@Purdue.edu</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wyss</LastName>
<ForeName>Phillip</ForeName>
<Initials>P</Initials>
</Author>
<Author ValidYN="Y"><LastName>Lazarus</LastName>
<ForeName>Sheryl A</ForeName>
<Initials>SA</Initials>
</Author>
<Author ValidYN="Y"><LastName>Shah</LastName>
<ForeName>Syed R</ForeName>
<Initials>SR</Initials>
</Author>
<Author ValidYN="Y"><LastName>Ren</LastName>
<ForeName>Wenhui</ForeName>
<Initials>W</Initials>
</Author>
<Author ValidYN="Y"><LastName>Szpankowski</LastName>
<ForeName>Wojciech</ForeName>
<Initials>W</Initials>
</Author>
<Author ValidYN="Y"><LastName>Crawford</LastName>
<ForeName>Gregory E</ForeName>
<Initials>GE</Initials>
</Author>
<Author ValidYN="Y"><LastName>Park</LastName>
<ForeName>Sang P</ForeName>
<Initials>SP</Initials>
</Author>
<Author ValidYN="Y"><LastName>Song</LastName>
<ForeName>Xiaohui C</ForeName>
<Initials>XC</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2008</Year>
<Month>12</Month>
<Day>30</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Genomics</MedlineTA>
<NlmUniqueID>8800135</NlmUniqueID>
<ISSNLinking>0888-7543</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018398">Homeodomain Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>157907-48-7</RegistryNumber>
<NameOfSubstance UI="C088144">HoxA protein</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>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002897" MajorTopicYN="N">Chromosomes, Human, Pair 7</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015894" MajorTopicYN="N">Genome, Human</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018398" MajorTopicYN="N">Homeodomain Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011401" MajorTopicYN="N">Promoter Regions, Genetic</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012045" MajorTopicYN="N">Regulatory Sequences, Nucleic Acid</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year>
<Month>10</Month>
<Day>15</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2008</Year>
<Month>05</Month>
<Day>28</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2008</Year>
<Month>11</Month>
<Day>17</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez"><Year>2008</Year>
<Month>12</Month>
<Day>17</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2008</Year>
<Month>12</Month>
<Day>17</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2009</Year>
<Month>4</Month>
<Day>16</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">19084590</ArticleId>
<ArticleId IdType="pii">S0888-7543(08)00302-9</ArticleId>
<ArticleId IdType="doi">10.1016/j.ygeno.2008.11.008</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Indiana</li>
</region>
</list>
<tree><noCountry><name sortKey="Crawford, Gregory E" sort="Crawford, Gregory E" uniqKey="Crawford G" first="Gregory E" last="Crawford">Gregory E. Crawford</name>
<name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name>
<name sortKey="Park, Sang P" sort="Park, Sang P" uniqKey="Park S" first="Sang P" last="Park">Sang P. Park</name>
<name sortKey="Ren, Wenhui" sort="Ren, Wenhui" uniqKey="Ren W" first="Wenhui" last="Ren">Wenhui Ren</name>
<name sortKey="Shah, Syed R" sort="Shah, Syed R" uniqKey="Shah S" first="Syed R" last="Shah">Syed R. Shah</name>
<name sortKey="Song, Xiaohui C" sort="Song, Xiaohui C" uniqKey="Song X" first="Xiaohui C" last="Song">Xiaohui C. Song</name>
<name sortKey="Szpankowski, Wojciech" sort="Szpankowski, Wojciech" uniqKey="Szpankowski W" first="Wojciech" last="Szpankowski">Wojciech Szpankowski</name>
<name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
</noCountry>
<country name="États-Unis"><region name="Indiana"><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
</region>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001F18 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 001F18 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Checkpoint |type= RBID |clé= pubmed:19084590 |texte= Discovering sequences with potential regulatory characteristics. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:19084590" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
![]() | This area was generated with Dilib version V0.6.33. | ![]() |