From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Identifieur interne : 000626 ( Ncbi/Checkpoint ); précédent : 000625; suivant : 000627From 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
Url:
DOI: 10.1371/journal.pone.0125000
PubMed: 25902288
PubMed Central: 4406561
Affiliations:
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<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>
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<affiliation wicri:level="2"><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>
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<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Hannink, Mark" sort="Hannink, Mark" uniqKey="Hannink M" first="Mark" last="Hannink">Mark Hannink</name>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Lubahn, Dennis B" sort="Lubahn, Dennis B" uniqKey="Lubahn D" first="Dennis B." last="Lubahn">Dennis B. Lubahn</name>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>MU Botanical Center, University of Missouri, Columbia, Missouri</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
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</affiliation>
</author>
<author><name sortKey="Birchler, James A" sort="Birchler, James A" uniqKey="Birchler J" first="James A." last="Birchler">James A. Birchler</name>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Biological Sciences, University of Missouri, Columbia, Missouri</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
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</author>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Computer Science Department, University of Missouri, Columbia, Missouri</wicri:regionArea>
<placeName><region type="state">Missouri (État)</region>
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</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
</placeName>
</affiliation>
<affiliation wicri:level="2"><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>
<placeName><region type="state">Missouri (État)</region>
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<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
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<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>
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<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
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<author><name sortKey="Goodson, M" uniqKey="Goodson M">M Goodson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hardcastle, Tj" uniqKey="Hardcastle T">TJ Hardcastle</name>
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<author><name sortKey="Kelly, Ka" uniqKey="Kelly K">KA Kelly</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Van De Wiel, Ma" uniqKey="Van De Wiel M">MA Van De Wiel</name>
</author>
<author><name sortKey="Leday, Gg" uniqKey="Leday G">GG Leday</name>
</author>
<author><name sortKey="Pardo, L" uniqKey="Pardo L">L Pardo</name>
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<author><name sortKey="Rue, H" uniqKey="Rue H">H Rue</name>
</author>
<author><name sortKey="Van Der Vaart, Aw" uniqKey="Van Der Vaart A">AW Van Der Vaart</name>
</author>
<author><name sortKey="Van Wieringen, Wn" uniqKey="Van Wieringen W">WN Van Wieringen</name>
</author>
</analytic>
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</author>
<author><name sortKey="Garcia Alcalde, F" uniqKey="Garcia Alcalde F">F García-Alcalde</name>
</author>
<author><name sortKey="Dopazo, J" uniqKey="Dopazo J">J Dopazo</name>
</author>
<author><name sortKey="Ferrer, A" uniqKey="Ferrer A">A Ferrer</name>
</author>
<author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Foster, Ba" uniqKey="Foster B">BA Foster</name>
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</author>
<author><name sortKey="Kwon, Ed" uniqKey="Kwon E">ED Kwon</name>
</author>
<author><name sortKey="Madias, C" uniqKey="Madias C">C Madias</name>
</author>
<author><name sortKey="Greenberg, Nm" uniqKey="Greenberg N">NM Greenberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mossine, Vv" uniqKey="Mossine V">VV Mossine</name>
</author>
<author><name sortKey="Mawhinney, Tp" uniqKey="Mawhinney T">TP Mawhinney</name>
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</analytic>
</biblStruct>
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</author>
<author><name sortKey="Patharkar, Or" uniqKey="Patharkar O">OR Patharkar</name>
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<author><name sortKey="Walker, Jc" uniqKey="Walker J">JC Walker</name>
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<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Missouri (État)</li>
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</list>
<tree><country name="États-Unis"><region name="Missouri (État)"><name sortKey="Li, Jilong" sort="Li, Jilong" uniqKey="Li J" first="Jilong" last="Li">Jilong Li</name>
</region>
<name sortKey="Birchler, James A" sort="Birchler, James A" uniqKey="Birchler J" first="James A." last="Birchler">James A. Birchler</name>
<name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name>
<name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name>
<name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name>
<name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name>
<name sortKey="Folk, William R" sort="Folk, William R" uniqKey="Folk W" first="William R." last="Folk">William R. Folk</name>
<name sortKey="Folk, William R" sort="Folk, William R" uniqKey="Folk W" first="William R." last="Folk">William R. Folk</name>
<name sortKey="Greenlief, C Michael" sort="Greenlief, C Michael" uniqKey="Greenlief C" first="C. Michael" last="Greenlief">C. Michael Greenlief</name>
<name sortKey="Greenlief, C Michael" sort="Greenlief, C Michael" uniqKey="Greenlief C" first="C. Michael" last="Greenlief">C. Michael Greenlief</name>
<name sortKey="Hannink, Mark" sort="Hannink, Mark" uniqKey="Hannink M" first="Mark" last="Hannink">Mark Hannink</name>
<name sortKey="Hannink, Mark" sort="Hannink, Mark" uniqKey="Hannink M" first="Mark" last="Hannink">Mark Hannink</name>
<name sortKey="Hou, Jie" sort="Hou, Jie" uniqKey="Hou J" first="Jie" last="Hou">Jie Hou</name>
<name sortKey="Li, Jilong" sort="Li, Jilong" uniqKey="Li J" first="Jilong" last="Li">Jilong Li</name>
<name sortKey="Lu, Yuan" sort="Lu, Yuan" uniqKey="Lu Y" first="Yuan" last="Lu">Yuan Lu</name>
<name sortKey="Lu, Yuan" sort="Lu, Yuan" uniqKey="Lu Y" first="Yuan" last="Lu">Yuan Lu</name>
<name sortKey="Lubahn, Dennis B" sort="Lubahn, Dennis B" uniqKey="Lubahn D" first="Dennis B." last="Lubahn">Dennis B. Lubahn</name>
<name sortKey="Lubahn, Dennis B" sort="Lubahn, Dennis B" uniqKey="Lubahn D" first="Dennis B." last="Lubahn">Dennis B. Lubahn</name>
<name sortKey="Mawhinney, Thomas P" sort="Mawhinney, Thomas P" uniqKey="Mawhinney T" first="Thomas P." last="Mawhinney">Thomas P. Mawhinney</name>
<name sortKey="Merideth, Benjamin Ryan" sort="Merideth, Benjamin Ryan" uniqKey="Merideth B" first="Benjamin Ryan" last="Merideth">Benjamin Ryan Merideth</name>
<name sortKey="Mossine, Valeri V" sort="Mossine, Valeri V" uniqKey="Mossine V" first="Valeri V." last="Mossine">Valeri V. Mossine</name>
<name sortKey="Mossine, Valeri V" sort="Mossine, Valeri V" uniqKey="Mossine V" first="Valeri V." last="Mossine">Valeri V. Mossine</name>
<name sortKey="Niederhuth, Chad E" sort="Niederhuth, Chad E" uniqKey="Niederhuth C" first="Chad E." last="Niederhuth">Chad E. Niederhuth</name>
<name sortKey="Sun, Lin" sort="Sun, Lin" uniqKey="Sun L" first="Lin" last="Sun">Lin Sun</name>
<name sortKey="Walker, John C" sort="Walker, John C" uniqKey="Walker J" first="John C." last="Walker">John C. Walker</name>
<name sortKey="Wilkins, Jordan Maximillian" sort="Wilkins, Jordan Maximillian" uniqKey="Wilkins J" first="Jordan Maximillian" last="Wilkins">Jordan Maximillian Wilkins</name>
</country>
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