From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Identifieur interne : 000073 ( Pmc/Curation ); précédent : 000072; suivant : 000074From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Auteurs : Jilong Li [États-Unis] ; Jie Hou [États-Unis] ; Lin Sun [États-Unis] ; Jordan Maximillian Wilkins [États-Unis] ; Yuan Lu [États-Unis] ; Chad E. Niederhuth [États-Unis] ; Benjamin Ryan Merideth [États-Unis] ; Thomas P. Mawhinney [États-Unis] ; Valeri V. Mossine [États-Unis] ; C. Michael Greenlief [États-Unis] ; John C. Walker [États-Unis] ; William R. Folk [États-Unis] ; Mark Hannink [États-Unis] ; Dennis B. Lubahn [États-Unis] ; James A. Birchler [États-Unis] ; Jianlin Cheng [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner—a multi-level bioinformatics protocol and pipeline—has been developed for such datasets. It includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from
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DOI: 10.1371/journal.pone.0125000
PubMed: 25902288
PubMed Central: 4406561
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Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>C. Bond Life Science Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25902288</idno><idno type="pmc">4406561</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406561</idno><idno type="RBID">PMC:4406561</idno><idno type="doi">10.1371/journal.pone.0125000</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000073</idno><idno type="wicri:Area/Pmc/Curation">000073</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data</title><author><name sortKey="Li, Jilong" sort="Li, Jilong" uniqKey="Li J" first="Jilong" last="Li">Jilong Li</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Computer Science Department, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science Department, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Hou, Jie" sort="Hou, Jie" uniqKey="Hou J" first="Jie" last="Hou">Jie Hou</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Computer Science Department, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science Department, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Sun, Lin" sort="Sun, Lin" uniqKey="Sun L" first="Lin" last="Sun">Lin Sun</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Wilkins, Jordan Maximillian" sort="Wilkins, Jordan Maximillian" uniqKey="Wilkins J" first="Jordan Maximillian" last="Wilkins">Jordan Maximillian Wilkins</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Lu, Yuan" sort="Lu, Yuan" uniqKey="Lu Y" first="Yuan" last="Lu">Yuan Lu</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Niederhuth, Chad E" sort="Niederhuth, Chad E" uniqKey="Niederhuth C" first="Chad E." last="Niederhuth">Chad E. Niederhuth</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Merideth, Benjamin Ryan" sort="Merideth, Benjamin Ryan" uniqKey="Merideth B" first="Benjamin Ryan" last="Merideth">Benjamin Ryan Merideth</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Mawhinney, Thomas P" sort="Mawhinney, Thomas P" uniqKey="Mawhinney T" first="Thomas P." last="Mawhinney">Thomas P. Mawhinney</name><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Mossine, Valeri V" sort="Mossine, Valeri V" uniqKey="Mossine V" first="Valeri V." last="Mossine">Valeri V. Mossine</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Greenlief, C Michael" sort="Greenlief, C Michael" uniqKey="Greenlief C" first="C. Michael" last="Greenlief">C. Michael Greenlief</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff005"><addr-line>Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Walker, John C" sort="Walker, John C" uniqKey="Walker J" first="John C." last="Walker">John C. Walker</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Folk, William R" sort="Folk, William R" uniqKey="Folk W" first="William R." last="Folk">William R. Folk</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Hannink, Mark" sort="Hannink, Mark" uniqKey="Hannink M" first="Mark" last="Hannink">Mark Hannink</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Lubahn, Dennis B" sort="Lubahn, Dennis B" uniqKey="Lubahn D" first="Dennis B." last="Lubahn">Dennis B. Lubahn</name><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff004"><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biochemistry, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Birchler, James A" sort="Birchler, James A" uniqKey="Birchler J" first="James A." last="Birchler">James A. Birchler</name><affiliation wicri:level="1"><nlm:aff id="aff003"><addr-line>Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Biological Sciences, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author><author><name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name><affiliation wicri:level="1"><nlm:aff id="aff001"><addr-line>Computer Science Department, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computer Science Department, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff002"><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff006"><addr-line>Informatics Institute, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Informatics Institute, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="aff007"><addr-line>C. Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>C. Bond Life Science Center, University of Missouri, Columbia, Missouri</wicri:regionArea></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner—a multi-level bioinformatics protocol and pipeline—has been developed for such datasets. It includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from <italic>Human</italic>, <italic>Mouse</italic>, <italic>Arabidopsis thaliana</italic>, and <italic>Drosophila melanogaster</italic> cells, and successfully identified differentially expressed genes, clustered them into cohesive functional groups, and constructed novel gene regulatory networks. The RNAMiner web service is available at <ext-link ext-link-type="uri" xlink:href="http://calla.rnet.missouri.edu/rnaminer/index.html">http://calla.rnet.missouri.edu/rnaminer/index.html</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Fang, Z" uniqKey="Fang Z">Z Fang</name></author><author><name sortKey="Martin, J" uniqKey="Martin J">J Martin</name></author><author><name sortKey="Wang, Z" uniqKey="Wang Z">Z Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Soneson, C" uniqKey="Soneson C">C Soneson</name></author><author><name sortKey="Delorenzi, M" uniqKey="Delorenzi M">M Delorenzi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Williams, Ba" uniqKey="Williams B">BA Williams</name></author><author><name sortKey="Mccue, K" uniqKey="Mccue K">K 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25902288</article-id><article-id pub-id-type="pmc">4406561</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0125000</article-id><article-id pub-id-type="publisher-id">PONE-D-14-38827</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data</article-title><alt-title alt-title-type="running-head">Mining Large RNA-Seq Data</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Li</surname><given-names>Jilong</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hou</surname><given-names>Jie</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sun</surname><given-names>Lin</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Wilkins</surname><given-names>Jordan Maximillian</given-names></name><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lu</surname><given-names>Yuan</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Niederhuth</surname><given-names>Chad E.</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Merideth</surname><given-names>Benjamin Ryan</given-names></name><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mawhinney</surname><given-names>Thomas P.</given-names></name><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mossine</surname><given-names>Valeri V.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Greenlief</surname><given-names>C. Michael</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff005"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Walker</surname><given-names>John C.</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Folk</surname><given-names>William R.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hannink</surname><given-names>Mark</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lubahn</surname><given-names>Dennis B.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff004"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Birchler</surname><given-names>James A.</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cheng</surname><given-names>Jianlin</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref ref-type="aff" rid="aff002"><sup>2</sup></xref><xref ref-type="aff" rid="aff006"><sup>6</sup></xref><xref ref-type="aff" rid="aff007"><sup>7</sup></xref><xref rid="cor001" ref-type="corresp">*</xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Computer Science Department, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff002"><label>2</label><addr-line>MU Botanical Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff004"><label>4</label><addr-line>Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff005"><label>5</label><addr-line>Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff006"><label>6</label><addr-line>Informatics Institute, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><aff id="aff007"><label>7</label><addr-line>C. Bond Life Science Center, University of Missouri, Columbia, Missouri, United States of America</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Provart</surname><given-names>Nicholas James</given-names></name><role>Academic Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Toronto, CANADA</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: JC JL. Performed the experiments: JC JL. Analyzed the data: JC JL. Contributed reagents/materials/analysis tools: JL LS JMW YL CEN BRM TPM VVM CMG JCW WRF MH DBL JAB JC. Wrote the paper: JL JC. Web service construction: JL JH.</p></fn><corresp id="cor001">* E-mail: <email>chengji@missouri.edu</email></corresp></author-notes><pub-date pub-type="epub"><day>22</day><month>4</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>10</volume><issue>4</issue><elocation-id>e0125000</elocation-id><history><date date-type="received"><day>28</day><month>8</month><year>2014</year></date><date date-type="accepted"><day>19</day><month>3</month><year>2015</year></date></history><permissions><copyright-year>2015</copyright-year><copyright-holder>Li et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0125000.pdf"></self-uri><abstract><p>RNA-Seq techniques generate hundreds of millions of short RNA reads using next-generation sequencing (NGS). These RNA reads can be mapped to reference genomes to investigate changes of gene expression but improved procedures for mining large RNA-Seq datasets to extract valuable biological knowledge are needed. RNAMiner—a multi-level bioinformatics protocol and pipeline—has been developed for such datasets. It includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed genes, predicting gene functions, and constructing gene regulatory networks. To demonstrate its utility, we applied RNAMiner to datasets generated from <italic>Human</italic>, <italic>Mouse</italic>, <italic>Arabidopsis thaliana</italic>, and <italic>Drosophila melanogaster</italic> cells, and successfully identified differentially expressed genes, clustered them into cohesive functional groups, and constructed novel gene regulatory networks. The RNAMiner web service is available at <ext-link ext-link-type="uri" xlink:href="http://calla.rnet.missouri.edu/rnaminer/index.html">http://calla.rnet.missouri.edu/rnaminer/index.html</ext-link>.</p></abstract><funding-group><funding-statement>The work was made possible by an NIH Botanical Center grant (P50AT006273) from the National Center for Complementary and Alternative Medicines (NCCAM), the Office of Dietary Supplements (ODS), and the National Cancer Institute (NCI), a NIH R01 grant (R01GM093123), and a NSF CAREER grant (DBI1149224). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NCCAM, ODS, NCI, the National Institutes of Health, or the National Science Foundation.</funding-statement></funding-group><counts><fig-count count="23"></fig-count><table-count count="9"></table-count><page-count count="30"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All of the six data sets used in this work are publicly available. The third, fourth, and fifth data sets have been deposited into the Gene Expression Omnibus (GEO) database (accession numbers: GSE41570, GSE41679, and GSE35288, respectively). The first, second, and sixth data sets are publicly available at <ext-link ext-link-type="uri" xlink:href="http://calla.rnet.missouri.edu/botanical/RNAMiner.html">http://calla.rnet.missouri.edu/botanical/RNAMiner.html</ext-link>.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All of the six data sets used in this work are publicly available. The third, fourth, and fifth data sets have been deposited into the Gene Expression Omnibus (GEO) database (accession numbers: GSE41570, GSE41679, and GSE35288, respectively). The first, second, and sixth data sets are publicly available at <ext-link ext-link-type="uri" xlink:href="http://calla.rnet.missouri.edu/botanical/RNAMiner.html">http://calla.rnet.missouri.edu/botanical/RNAMiner.html</ext-link>.</p></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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