Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.
Identifieur interne : 001849 ( PubMed/Corpus ); précédent : 001848; suivant : 001850Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.
Auteurs : Nung Kion Lee ; Pui Kwan Fong ; Mohd Tajuddin AbdullahSource :
- Bio-medical materials and engineering [ 1878-3619 ] ; 2014.
English descriptors
- KwdEn :
- Algorithms, Animals, Base Sequence, Chromosome Mapping (methods), Computer Simulation, Enhancer Elements, Genetic (genetics), Epigenesis, Genetic (genetics), Histones (genetics), Mice, Models, Genetic, Molecular Sequence Data, Pattern Recognition, Automated (methods), Sequence Analysis, DNA (methods).
- MESH :
- chemical , genetics : Histones.
- genetics : Enhancer Elements, Genetic, Epigenesis, Genetic.
- methods : Chromosome Mapping, Pattern Recognition, Automated, Sequence Analysis, DNA.
- Algorithms, Animals, Base Sequence, Computer Simulation, Mice, Models, Genetic, Molecular Sequence Data.
Abstract
Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features.
DOI: 10.3233/BME-141210
PubMed: 25227097
Links to Exploration step
pubmed:25227097Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.</title>
<author><name sortKey="Lee, Nung Kion" sort="Lee, Nung Kion" uniqKey="Lee N" first="Nung Kion" last="Lee">Nung Kion Lee</name>
<affiliation><nlm:affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Fong, Pui Kwan" sort="Fong, Pui Kwan" uniqKey="Fong P" first="Pui Kwan" last="Fong">Pui Kwan Fong</name>
<affiliation><nlm:affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Abdullah, Mohd Tajuddin" sort="Abdullah, Mohd Tajuddin" uniqKey="Abdullah M" first="Mohd Tajuddin" last="Abdullah">Mohd Tajuddin Abdullah</name>
<affiliation><nlm:affiliation>Center of Tasik Kenyir Ecosystem, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia.</nlm:affiliation>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2014">2014</date>
<idno type="RBID">pubmed:25227097</idno>
<idno type="pmid">25227097</idno>
<idno type="doi">10.3233/BME-141210</idno>
<idno type="wicri:Area/PubMed/Corpus">001849</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001849</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.</title>
<author><name sortKey="Lee, Nung Kion" sort="Lee, Nung Kion" uniqKey="Lee N" first="Nung Kion" last="Lee">Nung Kion Lee</name>
<affiliation><nlm:affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Fong, Pui Kwan" sort="Fong, Pui Kwan" uniqKey="Fong P" first="Pui Kwan" last="Fong">Pui Kwan Fong</name>
<affiliation><nlm:affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Abdullah, Mohd Tajuddin" sort="Abdullah, Mohd Tajuddin" uniqKey="Abdullah M" first="Mohd Tajuddin" last="Abdullah">Mohd Tajuddin Abdullah</name>
<affiliation><nlm:affiliation>Center of Tasik Kenyir Ecosystem, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia.</nlm:affiliation>
</affiliation>
</author>
</analytic>
<series><title level="j">Bio-medical materials and engineering</title>
<idno type="eISSN">1878-3619</idno>
<imprint><date when="2014" type="published">2014</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Base Sequence</term>
<term>Chromosome Mapping (methods)</term>
<term>Computer Simulation</term>
<term>Enhancer Elements, Genetic (genetics)</term>
<term>Epigenesis, Genetic (genetics)</term>
<term>Histones (genetics)</term>
<term>Mice</term>
<term>Models, Genetic</term>
<term>Molecular Sequence Data</term>
<term>Pattern Recognition, Automated (methods)</term>
<term>Sequence Analysis, DNA (methods)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Histones</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Enhancer Elements, Genetic</term>
<term>Epigenesis, Genetic</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term>
<term>Pattern Recognition, Automated</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Animals</term>
<term>Base Sequence</term>
<term>Computer Simulation</term>
<term>Mice</term>
<term>Models, Genetic</term>
<term>Molecular Sequence Data</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features. </div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25227097</PMID>
<DateCompleted><Year>2015</Year>
<Month>06</Month>
<Day>24</Day>
</DateCompleted>
<DateRevised><Year>2014</Year>
<Month>09</Month>
<Day>17</Day>
</DateRevised>
<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1878-3619</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>24</Volume>
<Issue>6</Issue>
<PubDate><Year>2014</Year>
</PubDate>
</JournalIssue>
<Title>Bio-medical materials and engineering</Title>
<ISOAbbreviation>Biomed Mater Eng</ISOAbbreviation>
</Journal>
<ArticleTitle>Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region.</ArticleTitle>
<Pagination><MedlinePgn>3807-14</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.3233/BME-141210</ELocationID>
<Abstract><AbstractText>Using Genetic Algorithm, this paper presents a modelling method to generate novel logical-based features from DNA sequences enriched with H3K4mel histone signatures. Current histone signature is mostly represented using k-mers content features incapable of representing all the possible complex interactions of various DNA segments. The main contributions are, among others: (a) demonstrating that there are complex interactions among sequence segments in the histone regions; (b) developing a parse tree representation of the logical complex features. The proposed novel feature is compared to the k-mers content features using datasets from the mouse (mm9) genome. Evaluation results show that the new feature improves the prediction performance as shown by f-measure for all datasets tested. Also, it is discovered that tree-based features generated from a single chromosome can be generalized to predict histone marks in other chromosomes not used in the training. These findings have a great impact on feature design considerations for histone signatures as well as other classifier design features. </AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lee</LastName>
<ForeName>Nung Kion</ForeName>
<Initials>NK</Initials>
<AffiliationInfo><Affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fong</LastName>
<ForeName>Pui Kwan</ForeName>
<Initials>PK</Initials>
<AffiliationInfo><Affiliation>Faculty of Cognitive Sciences and Human Development, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Abdullah</LastName>
<ForeName>Mohd Tajuddin</ForeName>
<Initials>MT</Initials>
<AffiliationInfo><Affiliation>Center of Tasik Kenyir Ecosystem, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo><Country>Netherlands</Country>
<MedlineTA>Biomed Mater Eng</MedlineTA>
<NlmUniqueID>9104021</NlmUniqueID>
<ISSNLinking>0959-2989</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D006657">Histones</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004742" MajorTopicYN="N">Enhancer Elements, Genetic</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D044127" MajorTopicYN="N">Epigenesis, Genetic</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006657" MajorTopicYN="N">Histones</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008957" MajorTopicYN="Y">Models, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010363" MajorTopicYN="N">Pattern Recognition, Automated</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Genetic algorithm</Keyword>
<Keyword MajorTopicYN="N">histone feature</Keyword>
<Keyword MajorTopicYN="N">tree-based feature</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year>
<Month>9</Month>
<Day>18</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed"><Year>2014</Year>
<Month>9</Month>
<Day>18</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline"><Year>2015</Year>
<Month>6</Month>
<Day>25</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">25227097</ArticleId>
<ArticleId IdType="pii">777638368Q3P3361</ArticleId>
<ArticleId IdType="doi">10.3233/BME-141210</ArticleId>
</ArticleIdList>
</PubmedData>
</pubmed>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001849 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 001849 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= PubMed |étape= Corpus |type= RBID |clé= pubmed:25227097 |texte= Modelling complex features from histone modification signatures using genetic algorithm for the prediction of enhancer region. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:25227097" \ | HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |