PMTED: a plant microRNA target expression database
Identifieur interne : 000D67 ( Main/Merge ); précédent : 000D66; suivant : 000D68PMTED: a plant microRNA target expression database
Auteurs : Xiuli Sun [République populaire de Chine] ; Boquan Dong [République populaire de Chine] ; Lingjie Yin [République populaire de Chine] ; Rongzhi Zhang [République populaire de Chine] ; Wei Du [République populaire de Chine] ; Dongfeng Liu [République populaire de Chine] ; Nan Shi [République populaire de Chine] ; Aili Li [République populaire de Chine] ; Yanchun Liang [République populaire de Chine] ; Long Mao [République populaire de Chine]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2013.
Abstract
MicroRNAs (miRNAs) are identified in nearly all plants where they play important roles in development and stress responses by target mRNA cleavage or translation repression. MiRNAs exert their functions by sequence complementation with target genes and hence their targets can be predicted using bioinformatics algorithms. In the past two decades, microarray technology has been employed to study genes involved in important biological processes such as biotic response, abiotic response, and specific tissues and developmental stages, many of which are miRNA targets. Despite their value in assisting research work for plant biologists, miRNA target genes are difficult to access without pre-processing and assistance of necessary analytical and visualization tools because they are embedded in a large body of microarray data that are scattered around in public databases.
Plant MiRNA Target Expression Database (PMTED) is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for miRNAs and their target sequences, gene ontology, and differential expression profiles. It also provides searching and browsing functions for a global Meta-network among species, bioprocesses, conditions, and miRNAs, meta-terms curated from well annotated microarray experiments. Networks are displayed through a Cytoscape Web-based graphical interface. In addition to conserved miRNAs, PMTED provides a target prediction portal for user-defined novel miRNAs and corresponding target expression profile retrieval. Hypotheses that are suggested by miRNA-target networks should provide starting points for further experimental validation.
PMTED exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets. PMTED will be updated over time and is freely available for non-commercial use at
Url:
DOI: 10.1186/1471-2105-14-174
PubMed: 23725466
PubMed Central: 3680227
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PMC:3680227Le document en format XML
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University, Changchun 130012, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012</wicri:regionArea><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region><region type="groupement">Dongbei</region></placeName><orgName type="university">Université de Jilin</orgName><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region></placeName></affiliation></author><author><name sortKey="Mao, Long" sort="Mao, Long" uniqKey="Mao L" first="Long" last="Mao">Long Mao</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop 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database</title><author><name sortKey="Sun, Xiuli" sort="Sun, Xiuli" uniqKey="Sun X" first="Xiuli" last="Sun">Xiuli Sun</name><affiliation wicri:level="4"><nlm:aff id="I1">Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012</wicri:regionArea><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region><region type="groupement">Dongbei</region></placeName><orgName type="university">Université de Jilin</orgName><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region></placeName></affiliation></author><author><name sortKey="Dong, Boquan" sort="Dong, Boquan" uniqKey="Dong B" first="Boquan" last="Dong">Boquan Dong</name><affiliation wicri:level="4"><nlm:aff id="I1">Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012</wicri:regionArea><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region><region type="groupement">Dongbei</region></placeName><orgName type="university">Université de Jilin</orgName><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region></placeName></affiliation></author><author><name sortKey="Yin, Lingjie" sort="Yin, Lingjie" uniqKey="Yin L" first="Lingjie" last="Yin">Lingjie Yin</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhang, Rongzhi" sort="Zhang, Rongzhi" uniqKey="Zhang R" first="Rongzhi" last="Zhang">Rongzhi Zhang</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Du, Wei" sort="Du, Wei" uniqKey="Du W" first="Wei" last="Du">Wei Du</name><affiliation wicri:level="4"><nlm:aff id="I1">Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012</wicri:regionArea><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region><region type="groupement">Dongbei</region></placeName><orgName type="university">Université de Jilin</orgName><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region></placeName></affiliation></author><author><name sortKey="Liu, Dongfeng" sort="Liu, Dongfeng" uniqKey="Liu D" first="Dongfeng" last="Liu">Dongfeng Liu</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Shi, Nan" sort="Shi, Nan" uniqKey="Shi N" first="Nan" last="Shi">Nan Shi</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Li, Aili" sort="Li, Aili" uniqKey="Li A" first="Aili" last="Li">Aili Li</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liang, Yanchun" sort="Liang, Yanchun" uniqKey="Liang Y" first="Yanchun" last="Liang">Yanchun Liang</name><affiliation wicri:level="4"><nlm:aff id="I1">Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012</wicri:regionArea><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region><region type="groupement">Dongbei</region></placeName><orgName type="university">Université de Jilin</orgName><placeName><settlement type="city">Changchun</settlement><region type="province">Jilin</region></placeName></affiliation></author><author><name sortKey="Mao, Long" sort="Mao, Long" uniqKey="Mao L" first="Long" last="Mao">Long Mao</name><affiliation wicri:level="1"><nlm:aff id="I2">Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>MicroRNAs (miRNAs) are identified in nearly all plants where they play important roles in development and stress responses by target mRNA cleavage or translation repression. MiRNAs exert their functions by sequence complementation with target genes and hence their targets can be predicted using bioinformatics algorithms. In the past two decades, microarray technology has been employed to study genes involved in important biological processes such as biotic response, abiotic response, and specific tissues and developmental stages, many of which are miRNA targets. Despite their value in assisting research work for plant biologists, miRNA target genes are difficult to access without pre-processing and assistance of necessary analytical and visualization tools because they are embedded in a large body of microarray data that are scattered around in public databases.</p></sec><sec><title>Description</title><p>Plant MiRNA Target Expression Database (PMTED) is designed to retrieve and analyze expression profiles of miRNA targets represented in the plethora of existing microarray data that are manually curated. It provides a Basic Information query function for miRNAs and their target sequences, gene ontology, and differential expression profiles. It also provides searching and browsing functions for a global Meta-network among species, bioprocesses, conditions, and miRNAs, meta-terms curated from well annotated microarray experiments. Networks are displayed through a Cytoscape Web-based graphical interface. In addition to conserved miRNAs, PMTED provides a target prediction portal for user-defined novel miRNAs and corresponding target expression profile retrieval. Hypotheses that are suggested by miRNA-target networks should provide starting points for further experimental validation.</p></sec><sec><title>Conclusions</title><p>PMTED exploits value-added microarray data to study the contextual significance of miRNA target genes and should assist functional investigation for both miRNAs and their targets. PMTED will be updated over time and is freely available for non-commercial use at <ext-link ext-link-type="uri" xlink:href="http://pmted.agrinome.org">http://pmted.agrinome.org</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Khraiwesh, B" uniqKey="Khraiwesh B">B Khraiwesh</name></author><author><name sortKey="Zhu, Jk" uniqKey="Zhu J">JK Zhu</name></author><author><name sortKey="Zhu, J" uniqKey="Zhu J">J Zhu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths-Jones</name></author><author><name sortKey="Saini, Hk" uniqKey="Saini H">HK Saini</name></author><author><name sortKey="Van Dongen, S" uniqKey="Van Dongen S">S Van Dongen</name></author><author><name sortKey="Enright, Aj" uniqKey="Enright A">AJ Enright</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Parkinson, H" uniqKey="Parkinson 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