Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.
Identifieur interne : 001602 ( Main/Exploration ); précédent : 001601; suivant : 001603Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.
Auteurs : Ezzeddin Kamil Mohamed Hashim [Malaisie] ; Rosni Abdullah [Malaisie]Source :
- Journal of theoretical biology [ 1095-8541 ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA.
- chemistry : Chromosomes, Human, Pair 21.
- genetics : Birds, CpG Islands, Fishes, Mammals, Nucleotide Motifs.
- Animals, Computational Biology, Databases, Genetic, Humans, Promoter Regions, Genetic.
Abstract
Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets.
DOI: 10.1016/j.jtbi.2015.09.014
PubMed: 26427337
Affiliations:
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Electronic address: ezzeddin@usm.my.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang</wicri:regionArea><wicri:noRegion>Penang</wicri:noRegion></affiliation></author><author><name sortKey="Abdullah, Rosni" sort="Abdullah, Rosni" uniqKey="Abdullah R" first="Rosni" last="Abdullah">Rosni Abdullah</name><affiliation wicri:level="1"><nlm:affiliation>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia; National Advanced IPv6 Centre of Excellence (NAv6), School of Computer Sciences Building, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia; National Advanced IPv6 Centre of Excellence (NAv6), School of Computer Sciences Building, Universiti Sains Malaysia, 11800 Gelugor, Penang</wicri:regionArea><wicri:noRegion>Penang</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26427337</idno><idno type="pmid">26427337</idno><idno type="doi">10.1016/j.jtbi.2015.09.014</idno><idno type="wicri:Area/PubMed/Corpus">001447</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001447</idno><idno type="wicri:Area/PubMed/Curation">001447</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001447</idno><idno type="wicri:Area/PubMed/Checkpoint">001375</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001375</idno><idno type="wicri:Area/Ncbi/Merge">001290</idno><idno type="wicri:Area/Ncbi/Curation">001290</idno><idno type="wicri:Area/Ncbi/Checkpoint">001290</idno><idno type="wicri:Area/Main/Merge">001607</idno><idno type="wicri:Area/Main/Curation">001602</idno><idno type="wicri:Area/Main/Exploration">001602</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.</title><author><name sortKey="Mohamed Hashim, Ezzeddin Kamil" sort="Mohamed Hashim, Ezzeddin Kamil" uniqKey="Mohamed Hashim E" first="Ezzeddin Kamil" last="Mohamed Hashim">Ezzeddin Kamil Mohamed Hashim</name><affiliation wicri:level="1"><nlm:affiliation>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia. Electronic address: ezzeddin@usm.my.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang</wicri:regionArea><wicri:noRegion>Penang</wicri:noRegion></affiliation></author><author><name sortKey="Abdullah, Rosni" sort="Abdullah, Rosni" uniqKey="Abdullah R" first="Rosni" last="Abdullah">Rosni Abdullah</name><affiliation wicri:level="1"><nlm:affiliation>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia; National Advanced IPv6 Centre of Excellence (NAv6), School of Computer Sciences Building, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>School of Computer Sciences, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia; National Advanced IPv6 Centre of Excellence (NAv6), School of Computer Sciences Building, Universiti Sains Malaysia, 11800 Gelugor, Penang</wicri:regionArea><wicri:noRegion>Penang</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of theoretical biology</title><idno type="eISSN">1095-8541</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Birds (genetics)</term><term>Chromosomes, Human, Pair 21 (chemistry)</term><term>Computational Biology</term><term>CpG Islands (genetics)</term><term>DNA (genetics)</term><term>Databases, Genetic</term><term>Fishes (genetics)</term><term>Humans</term><term>Mammals (genetics)</term><term>Nucleotide Motifs (genetics)</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>Animaux</term><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Chromosomes humains de la paire 21 ()</term><term>Humains</term><term>Ilots CpG (génétique)</term><term>Mammifères (génétique)</term><term>Motifs nucléotidiques (génétique)</term><term>Oiseaux (génétique)</term><term>Poissons (génétique)</term><term>Régions promotrices (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Chromosomes, Human, Pair 21</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Birds</term><term>CpG Islands</term><term>Fishes</term><term>Mammals</term><term>Nucleotide Motifs</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Ilots CpG</term><term>Mammifères</term><term>Motifs nucléotidiques</term><term>Oiseaux</term><term>Poissons</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Computational Biology</term><term>Databases, Genetic</term><term>Humans</term><term>Promoter Regions, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Chromosomes humains de la paire 21</term><term>Humains</term><term>Régions promotrices (génétique)</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets. </div></front></TEI><affiliations><list><country><li>Malaisie</li></country></list><tree><country name="Malaisie"><noRegion><name sortKey="Mohamed Hashim, Ezzeddin Kamil" sort="Mohamed Hashim, Ezzeddin Kamil" uniqKey="Mohamed Hashim E" first="Ezzeddin Kamil" last="Mohamed Hashim">Ezzeddin Kamil Mohamed Hashim</name></noRegion><name sortKey="Abdullah, Rosni" sort="Abdullah, Rosni" uniqKey="Abdullah R" first="Rosni" last="Abdullah">Rosni Abdullah</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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