A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)
Identifieur interne : 000926 ( Main/Exploration ); précédent : 000925; suivant : 000927A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)
Auteurs : Yuki Iwasaki [Japon] ; Takashi Abe [Japon] ; Kennosuke Wada ; Yoshiko Wada [Japon] ; Toshimichi IkemuraSource :
- Microorganisms [ 2076-2607 ] ; 2013.
Abstract
With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.
Url:
DOI: 10.3390/microorganisms1010137
PubMed: 27694768
PubMed Central: 5029494
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)</title><author><name sortKey="Iwasaki, Yuki" sort="Iwasaki, Yuki" uniqKey="Iwasaki Y" first="Yuki" last="Iwasaki">Yuki Iwasaki</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-microorganisms-01-00137">Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Abe, Takashi" sort="Abe, Takashi" uniqKey="Abe T" first="Takashi" last="Abe">Takashi Abe</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; 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E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-microorganisms-01-00137">Faculty of Medicine, Shiga University of Medical Science, Shiga-ken 520-2121, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Faculty of Medicine, Shiga University of Medical Science, Shiga-ken 520-2121</wicri:regionArea><wicri:noRegion>Shiga-ken 520-2121</wicri:noRegion></affiliation></author><author><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27694768</idno><idno type="pmc">5029494</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5029494</idno><idno type="RBID">PMC:5029494</idno><idno type="doi">10.3390/microorganisms1010137</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000E01</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000E01</idno><idno type="wicri:Area/Pmc/Curation">000E01</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000E01</idno><idno type="wicri:Area/Pmc/Checkpoint">000659</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000659</idno><idno type="wicri:Area/Ncbi/Merge">000D08</idno><idno type="wicri:Area/Ncbi/Curation">000D08</idno><idno type="wicri:Area/Ncbi/Checkpoint">000D08</idno><idno type="wicri:Area/Main/Merge">000927</idno><idno type="wicri:Area/Main/Curation">000926</idno><idno type="wicri:Area/Main/Exploration">000926</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)</title><author><name sortKey="Iwasaki, Yuki" sort="Iwasaki, Yuki" uniqKey="Iwasaki Y" first="Yuki" last="Iwasaki">Yuki Iwasaki</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af2-microorganisms-01-00137">Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Abe, Takashi" sort="Abe, Takashi" uniqKey="Abe T" first="Takashi" last="Abe">Takashi Abe</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af3-microorganisms-01-00137">Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata-ken 950-2181, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata-ken 950-2181</wicri:regionArea><wicri:noRegion>Niigata-ken 950-2181</wicri:noRegion></affiliation></author><author><name sortKey="Wada, Kennosuke" sort="Wada, Kennosuke" uniqKey="Wada K" first="Kennosuke" last="Wada">Kennosuke Wada</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation></author><author><name sortKey="Wada, Yoshiko" sort="Wada, Yoshiko" uniqKey="Wada Y" first="Yoshiko" last="Wada">Yoshiko Wada</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-microorganisms-01-00137">Faculty of Medicine, Shiga University of Medical Science, Shiga-ken 520-2121, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Faculty of Medicine, Shiga University of Medical Science, Shiga-ken 520-2121</wicri:regionArea><wicri:noRegion>Shiga-ken 520-2121</wicri:noRegion></affiliation></author><author><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><affiliation><nlm:aff id="af1-microorganisms-01-00137">Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama-shi, Shiga-ken 526-0829, Japan; E-Mails:<email>b105023@nagahama-i-bio.ac.jp</email> (Y.I.);<email>k_wada@nagahama-i-bio.ac.jp</email> (K.W.);<email>y_wada@nagahama-i-bio.ac.jp</email> (Y.W.);<email>t_ikemura@nagahama-i-bio.ac.jp</email> (T.I.)</nlm:aff></affiliation></author></analytic><series><title level="j">Microorganisms</title><idno type="eISSN">2076-2607</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>With the remarkable increase of genomic sequence data of microorganisms, novel tools are needed for comprehensive analyses of the big sequence data available. The self-organizing map (SOM) is an effective tool for clustering and visualizing high-dimensional data, such as oligonucleotide composition on one map. By modifying the conventional SOM, we developed batch-learning SOM (BLSOM), which allowed classification of sequence fragments (e.g., 1 kb) according to phylotypes, solely depending on oligonucleotide composition. Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes important in life sciences. BLSOM is most suitable for phylogenetic assignment of metagenomic sequences, because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition. We first constructed oligonucleotide BLSOMs for all available sequences from genomes of known species, and by mapping metagenomic sequences on these large-scale BLSOMs, we can predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms, including viruses. BLSOM has shown that influenza viruses isolated from humans and birds clearly differ in oligonucleotide composition. Based on this host-dependent oligonucleotide composition, we have proposed strategies for predicting directional changes of virus sequences and for surveilling potentially hazardous strains when introduced into humans from non-human sources.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Nei, M" uniqKey="Nei M">M. Nei</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kumar, S" uniqKey="Kumar S">S. 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Nakamura</name></author><author><name sortKey="Altaf Ul Amin, M" uniqKey="Altaf Ul Amin M">M. Altaf-Ul-Amin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement></list><tree><noCountry><name sortKey="Ikemura, Toshimichi" sort="Ikemura, Toshimichi" uniqKey="Ikemura T" first="Toshimichi" last="Ikemura">Toshimichi Ikemura</name><name sortKey="Wada, Kennosuke" sort="Wada, Kennosuke" uniqKey="Wada K" first="Kennosuke" last="Wada">Kennosuke Wada</name></noCountry><country name="Japon"><region name="Région de Kantō"><name sortKey="Iwasaki, Yuki" sort="Iwasaki, Yuki" uniqKey="Iwasaki Y" first="Yuki" last="Iwasaki">Yuki Iwasaki</name></region><name sortKey="Abe, Takashi" sort="Abe, Takashi" uniqKey="Abe T" first="Takashi" last="Abe">Takashi Abe</name><name sortKey="Wada, Yoshiko" sort="Wada, Yoshiko" uniqKey="Wada Y" first="Yoshiko" last="Wada">Yoshiko Wada</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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