PlantNATsDB: a comprehensive database of plant natural antisense transcripts
Identifieur interne : 001692 ( Main/Merge ); précédent : 001691; suivant : 001693PlantNATsDB: a comprehensive database of plant natural antisense transcripts
Auteurs : Dijun Chen [République populaire de Chine] ; Chunhui Yuan [République populaire de Chine] ; Jian Zhang [République populaire de Chine] ; Zhao Zhang [République populaire de Chine] ; Lin Bai [République populaire de Chine] ; Yijun Meng [République populaire de Chine] ; Ling-Ling Chen [République populaire de Chine] ; Ming Chen [République populaire de Chine]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2011.
Abstract
Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at
Url:
DOI: 10.1093/nar/gkr823
PubMed: 22058132
PubMed Central: 3245084
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PMC:3245084Le document en format XML
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China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Yuan, Chunhui" sort="Yuan, Chunhui" uniqKey="Yuan C" first="Chunhui" last="Yuan">Chunhui Yuan</name><affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="gkr823-AFF1">Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058</nlm:aff><orgName type="university">Université de Zhejiang</orgName><country>République populaire de Chine</country><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Zhang, Jian" sort="Zhang, Jian" uniqKey="Zhang J" first="Jian" last="Zhang">Jian Zhang</name><affiliation wicri:level="1"><nlm:aff id="gkr823-AFF1">State Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Zhao" sort="Zhang, Zhao" uniqKey="Zhang Z" first="Zhao" last="Zhang">Zhao Zhang</name><affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="gkr823-AFF1">Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058</nlm:aff><orgName type="university">Université de Zhejiang</orgName><country>République populaire de Chine</country><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Bai, Lin" sort="Bai, Lin" uniqKey="Bai L" first="Lin" last="Bai">Lin Bai</name><affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="gkr823-AFF1">Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058</nlm:aff><orgName type="university">Université de Zhejiang</orgName><country>République populaire de Chine</country><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Meng, Yijun" sort="Meng, Yijun" uniqKey="Meng Y" first="Yijun" last="Meng">Yijun Meng</name><affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="gkr823-AFF1">Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058</nlm:aff><orgName type="university">Université de Zhejiang</orgName><country>République populaire de Chine</country><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Chen, Ling Ling" sort="Chen, Ling Ling" uniqKey="Chen L" first="Ling-Ling" last="Chen">Ling-Ling Chen</name><affiliation wicri:level="1"><nlm:aff id="gkr823-AFF1">State Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China</nlm:aff><country xml:lang="fr" wicri:curation="lc">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070</wicri:regionArea><wicri:noRegion>430070</wicri:noRegion></affiliation></author><author><name sortKey="Chen, Ming" sort="Chen, Ming" uniqKey="Chen M" first="Ming" last="Chen">Ming Chen</name><affiliation wicri:level="4"><nlm:aff wicri:cut=" and" id="gkr823-AFF1">Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058</nlm:aff><orgName type="university">Université de Zhejiang</orgName><country>République populaire de Chine</country><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at <ext-link ext-link-type="uri" xlink:href="http://bis.zju.edu.cn/pnatdb/">http://bis.zju.edu.cn/pnatdb/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ponting, Cp" uniqKey="Ponting C">CP Ponting</name></author><author><name sortKey="Oliver, Pl" uniqKey="Oliver P">PL Oliver</name></author><author><name sortKey="Reik, W" uniqKey="Reik W">W Reik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brosnan, Ca" uniqKey="Brosnan C">CA Brosnan</name></author><author><name sortKey="Voinnet, O" uniqKey="Voinnet O">O Voinnet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ghildiyal, M" uniqKey="Ghildiyal M">M Ghildiyal</name></author><author><name sortKey="Zamore, Pd" uniqKey="Zamore P">PD Zamore</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mercer, Tr" uniqKey="Mercer T">TR 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Addo-Quaye</name></author><author><name sortKey="Eshoo, Tw" uniqKey="Eshoo T">TW Eshoo</name></author><author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name></author><author><name sortKey="Axtell, Mj" uniqKey="Axtell M">MJ Axtell</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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