PMTED: a plant microRNA target expression database
Identifieur interne : 000A87 ( Pmc/Curation ); précédent : 000A86; suivant : 000A88PMTED: 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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<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>
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<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 H">H Parkinson</name>
</author>
<author><name sortKey="Kapushesky, M" uniqKey="Kapushesky M">M Kapushesky</name>
</author>
<author><name sortKey="Shojatalab, M" uniqKey="Shojatalab M">M Shojatalab</name>
</author>
<author><name sortKey="Abeygunawardena, N" uniqKey="Abeygunawardena N">N Abeygunawardena</name>
</author>
<author><name sortKey="Coulson, R" uniqKey="Coulson R">R Coulson</name>
</author>
<author><name sortKey="Farne, A" uniqKey="Farne A">A Farne</name>
</author>
<author><name sortKey="Holloway, E" uniqKey="Holloway E">E Holloway</name>
</author>
<author><name sortKey="Kolesnykov, N" uniqKey="Kolesnykov N">N Kolesnykov</name>
</author>
<author><name sortKey="Lilja, P" uniqKey="Lilja P">P Lilja</name>
</author>
<author><name sortKey="Lukk, M" uniqKey="Lukk M">M Lukk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Parkinson, H" uniqKey="Parkinson H">H Parkinson</name>
</author>
<author><name sortKey="Sarkans, U" uniqKey="Sarkans U">U Sarkans</name>
</author>
<author><name sortKey="Shojatalab, M" uniqKey="Shojatalab M">M Shojatalab</name>
</author>
<author><name sortKey="Abeygunawardena, N" uniqKey="Abeygunawardena N">N Abeygunawardena</name>
</author>
<author><name sortKey="Contrino, S" uniqKey="Contrino S">S Contrino</name>
</author>
<author><name sortKey="Coulson, R" uniqKey="Coulson R">R Coulson</name>
</author>
<author><name sortKey="Farne, A" uniqKey="Farne A">A Farne</name>
</author>
<author><name sortKey="Garcia Lara, G" uniqKey="Garcia Lara G">G Garcia Lara</name>
</author>
<author><name sortKey="Holloway, E" uniqKey="Holloway E">E Holloway</name>
</author>
<author><name sortKey="Kapushesky, M" uniqKey="Kapushesky M">M Kapushesky</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Edgar, R" uniqKey="Edgar R">R Edgar</name>
</author>
<author><name sortKey="Domrachev, M" uniqKey="Domrachev M">M Domrachev</name>
</author>
<author><name sortKey="Lash, Ae" uniqKey="Lash A">AE Lash</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bulow, L" uniqKey="Bulow L">L Bülow</name>
</author>
<author><name sortKey="Schindler, M" uniqKey="Schindler M">M Schindler</name>
</author>
<author><name sortKey="Choi, C" uniqKey="Choi C">C Choi</name>
</author>
<author><name sortKey="Hehl, R" uniqKey="Hehl R">R Hehl</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lohse, M" uniqKey="Lohse M">M Lohse</name>
</author>
<author><name sortKey="Nunes Nesi, A" uniqKey="Nunes Nesi A">A Nunes Nesi</name>
</author>
<author><name sortKey="Kruger, P" uniqKey="Kruger P">P Kruger</name>
</author>
<author><name sortKey="Nagel, A" uniqKey="Nagel A">A Nagel</name>
</author>
<author><name sortKey="Hannemann, J" uniqKey="Hannemann J">J Hannemann</name>
</author>
<author><name sortKey="Giorgi, Fm" uniqKey="Giorgi F">FM Giorgi</name>
</author>
<author><name sortKey="Childs, L" uniqKey="Childs L">L Childs</name>
</author>
<author><name sortKey="Osorio, S" uniqKey="Osorio S">S Osorio</name>
</author>
<author><name sortKey="Walther, D" uniqKey="Walther D">D Walther</name>
</author>
<author><name sortKey="Selbig, J" uniqKey="Selbig J">J Selbig</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Irizarry, Ra" uniqKey="Irizarry R">RA Irizarry</name>
</author>
<author><name sortKey="Hobbs, B" uniqKey="Hobbs B">B Hobbs</name>
</author>
<author><name sortKey="Collin, F" uniqKey="Collin F">F Collin</name>
</author>
<author><name sortKey="Beazer Barclay, Yd" uniqKey="Beazer Barclay Y">YD Beazer-Barclay</name>
</author>
<author><name sortKey="Antonellis, Kj" uniqKey="Antonellis K">KJ Antonellis</name>
</author>
<author><name sortKey="Scherf, U" uniqKey="Scherf U">U Scherf</name>
</author>
<author><name sortKey="Speed, Tp" uniqKey="Speed T">TP Speed</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhang, Z" uniqKey="Zhang Z">Z Zhang</name>
</author>
<author><name sortKey="Yu, J" uniqKey="Yu J">J Yu</name>
</author>
<author><name sortKey="Li, D" uniqKey="Li D">D Li</name>
</author>
<author><name sortKey="Liu, F" uniqKey="Liu F">F Liu</name>
</author>
<author><name sortKey="Zhou, X" uniqKey="Zhou X">X Zhou</name>
</author>
<author><name sortKey="Wang, T" uniqKey="Wang T">T Wang</name>
</author>
<author><name sortKey="Ling, Y" uniqKey="Ling Y">Y Ling</name>
</author>
<author><name sortKey="Su, Z" uniqKey="Su Z">Z Su</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Allen, E" uniqKey="Allen E">E Allen</name>
</author>
<author><name sortKey="Xie, Z" uniqKey="Xie Z">Z Xie</name>
</author>
<author><name sortKey="Gustafson, Am" uniqKey="Gustafson A">AM Gustafson</name>
</author>
<author><name sortKey="Carrington, Jc" uniqKey="Carrington J">JC Carrington</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dai, X" uniqKey="Dai X">X Dai</name>
</author>
<author><name sortKey="Zhao, Px" uniqKey="Zhao P">PX Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhou, M" uniqKey="Zhou M">M Zhou</name>
</author>
<author><name sortKey="Gu, L" uniqKey="Gu L">L Gu</name>
</author>
<author><name sortKey="Li, P" uniqKey="Li P">P Li</name>
</author>
<author><name sortKey="Song, X" uniqKey="Song X">X Song</name>
</author>
<author><name sortKey="Wei, L" uniqKey="Wei L">L Wei</name>
</author>
<author><name sortKey="Chen, Z" uniqKey="Chen Z">Z Chen</name>
</author>
<author><name sortKey="Cao, X" uniqKey="Cao X">X Cao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smyth, Gk" uniqKey="Smyth G">GK Smyth</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lopes, Ct" uniqKey="Lopes C">CT Lopes</name>
</author>
<author><name sortKey="Franz, M" uniqKey="Franz M">M Franz</name>
</author>
<author><name sortKey="Kazi, F" uniqKey="Kazi F">F Kazi</name>
</author>
<author><name sortKey="Donaldson, Sl" uniqKey="Donaldson S">SL Donaldson</name>
</author>
<author><name sortKey="Morris, Q" uniqKey="Morris Q">Q Morris</name>
</author>
<author><name sortKey="Bader, Gd" uniqKey="Bader G">GD Bader</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sunkar, R" uniqKey="Sunkar R">R Sunkar</name>
</author>
<author><name sortKey="Girke, T" uniqKey="Girke T">T Girke</name>
</author>
<author><name sortKey="Jain, Pk" uniqKey="Jain P">PK Jain</name>
</author>
<author><name sortKey="Zhu, J K" uniqKey="Zhu J">J-K Zhu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kantar, M" uniqKey="Kantar M">M Kantar</name>
</author>
<author><name sortKey="Lucas, Sj" uniqKey="Lucas S">SJ Lucas</name>
</author>
<author><name sortKey="Budak, H" uniqKey="Budak H">H Budak</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Szcze Niak, Mw" uniqKey="Szcze Niak M">MW Szcześniak</name>
</author>
<author><name sortKey="Deorowicz, S" uniqKey="Deorowicz S">S Deorowicz</name>
</author>
<author><name sortKey="Gapski, J" uniqKey="Gapski J">J Gapski</name>
</author>
<author><name sortKey="Kaczy Ski, L" uniqKey="Kaczy Ski L">L Kaczyński</name>
</author>
<author><name sortKey="Makalowska, I" uniqKey="Makalowska I">I Makałowska</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bielewicz, D" uniqKey="Bielewicz D">D Bielewicz</name>
</author>
<author><name sortKey="Dolata, J" uniqKey="Dolata J">J Dolata</name>
</author>
<author><name sortKey="Zielezinski, A" uniqKey="Zielezinski A">A Zielezinski</name>
</author>
<author><name sortKey="Alaba, S" uniqKey="Alaba S">S Alaba</name>
</author>
<author><name sortKey="Szarzynska, B" uniqKey="Szarzynska B">B Szarzynska</name>
</author>
<author><name sortKey="Szczesniak, Mw" uniqKey="Szczesniak M">MW Szczesniak</name>
</author>
<author><name sortKey="Jarmolowski, A" uniqKey="Jarmolowski A">A Jarmolowski</name>
</author>
<author><name sortKey="Szweykowska Kulinska, Z" uniqKey="Szweykowska Kulinska Z">Z Szweykowska-Kulinska</name>
</author>
<author><name sortKey="Karlowski, Wm" uniqKey="Karlowski W">WM Karlowski</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths Jones</name>
</author>
<author><name sortKey="Grocock, Rj" uniqKey="Grocock R">RJ Grocock</name>
</author>
<author><name sortKey="Van Dongen, S" uniqKey="Van Dongen S">S Van Dongen</name>
</author>
<author><name sortKey="Bateman, A" uniqKey="Bateman A">A Bateman</name>
</author>
<author><name sortKey="Enright, Aj" uniqKey="Enright A">AJ Enright</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lewis, Bp" uniqKey="Lewis B">BP Lewis</name>
</author>
<author><name sortKey="Burge, Cb" uniqKey="Burge C">CB Burge</name>
</author>
<author><name sortKey="Bartel, Dp" uniqKey="Bartel D">DP Bartel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sethupathy, P" uniqKey="Sethupathy P">P Sethupathy</name>
</author>
<author><name sortKey="Corda, B" uniqKey="Corda B">B Corda</name>
</author>
<author><name sortKey="Hatzigeorgiou, Ag" uniqKey="Hatzigeorgiou A">AG Hatzigeorgiou</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yang, Jh" uniqKey="Yang J">JH Yang</name>
</author>
<author><name sortKey="Li, Jh" uniqKey="Li J">JH Li</name>
</author>
<author><name sortKey="Shao, P" uniqKey="Shao P">P Shao</name>
</author>
<author><name sortKey="Zhou, H" uniqKey="Zhou H">H Zhou</name>
</author>
<author><name sortKey="Chen, Yq" uniqKey="Chen Y">YQ Chen</name>
</author>
<author><name sortKey="Qu, Lh" uniqKey="Qu L">LH Qu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kozomara, A" uniqKey="Kozomara A">A Kozomara</name>
</author>
<author><name sortKey="Griffiths Jones, S" uniqKey="Griffiths Jones S">S Griffiths Jones</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hennig, L" uniqKey="Hennig L">L Hennig</name>
</author>
<author><name sortKey="Menges, M" uniqKey="Menges M">M Menges</name>
</author>
<author><name sortKey="Murray, Jah" uniqKey="Murray J">JAH Murray</name>
</author>
<author><name sortKey="Gruissem, W" uniqKey="Gruissem W">W Gruissem</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Redman, Jc" uniqKey="Redman J">JC Redman</name>
</author>
<author><name sortKey="Haas, Bj" uniqKey="Haas B">BJ Haas</name>
</author>
<author><name sortKey="Tanimoto, G" uniqKey="Tanimoto G">G Tanimoto</name>
</author>
<author><name sortKey="Town, Cd" uniqKey="Town C">CD Town</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<journal-id journal-id-type="iso-abbrev">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23725466</article-id>
<article-id pub-id-type="pmc">3680227</article-id>
<article-id pub-id-type="publisher-id">1471-2105-14-174</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-14-174</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Database</subject>
</subj-group>
</article-categories>
<title-group><article-title>PMTED: a plant microRNA target expression database</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" id="A1"><name><surname>Sun</surname>
<given-names>Xiuli</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>xiuli.sun.1980@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Dong</surname>
<given-names>Boquan</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>d_b_q@163.com</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Yin</surname>
<given-names>Lingjie</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>bluebear1211@gmail.com</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Zhang</surname>
<given-names>Rongzhi</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>zhangrongzhi1981@126.com</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Du</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>dwtyfx@hotmail.com</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Liu</surname>
<given-names>Dongfeng</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>ldf0909@163.com</email>
</contrib>
<contrib contrib-type="author" id="A7"><name><surname>Shi</surname>
<given-names>Nan</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>iamshinan@qq.com</email>
</contrib>
<contrib contrib-type="author" id="A8"><name><surname>Li</surname>
<given-names>Aili</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>liaili@caas.cn</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A9"><name><surname>Liang</surname>
<given-names>Yanchun</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>ycliang@jlu.edu.cn</email>
</contrib>
<contrib contrib-type="author" corresp="yes" id="A10"><name><surname>Mao</surname>
<given-names>Long</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>maolong@caas.cn</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China</aff>
<aff id="I2"><label>2</label>
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China</aff>
<pub-date pub-type="collection"><year>2013</year>
</pub-date>
<pub-date pub-type="epub"><day>3</day>
<month>6</month>
<year>2013</year>
</pub-date>
<volume>14</volume>
<fpage>174</fpage>
<lpage>174</lpage>
<history><date date-type="received"><day>8</day>
<month>11</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>30</day>
<month>5</month>
<year>2013</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2013 Sun et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2013</copyright-year>
<copyright-holder>Sun et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/14/174"></self-uri>
<abstract><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>
</abstract>
<kwd-group><kwd>MiRNA</kwd>
<kwd>Microarray</kwd>
<kwd>Meta-analysis</kwd>
<kwd>Stress response</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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