From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data
Identifieur interne : 000111 ( Main/Merge ); précédent : 000110; suivant : 000112From 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
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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. 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Niederhuth</name><affiliation wicri:level="2"><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><placeName><region type="state">Missouri (État)</region></placeName></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="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="Mawhinney, Thomas P" sort="Mawhinney, Thomas P" uniqKey="Mawhinney T" first="Thomas P." last="Mawhinney">Thomas P. Mawhinney</name><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="Mossine, Valeri V" sort="Mossine, Valeri V" uniqKey="Mossine V" first="Valeri V." last="Mossine">Valeri V. Mossine</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="Greenlief, C Michael" sort="Greenlief, C Michael" uniqKey="Greenlief C" first="C. Michael" last="Greenlief">C. Michael Greenlief</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="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><placeName><region type="state">Missouri (État)</region></placeName></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="2"><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><placeName><region type="state">Missouri (État)</region></placeName></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="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="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><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="Birchler, James A" sort="Birchler, James A" uniqKey="Birchler J" first="James A." last="Birchler">James A. Birchler</name><affiliation wicri:level="2"><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><placeName><region type="state">Missouri (État)</region></placeName></affiliation></author><author><name sortKey="Cheng, Jianlin" sort="Cheng, Jianlin" uniqKey="Cheng J" first="Jianlin" last="Cheng">Jianlin Cheng</name><affiliation wicri:level="2"><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><placeName><region type="state">Missouri (État)</region></placeName></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></placeName></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. 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