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When analyzing transcriptional regulation using AthaMap it may be important to learn which genes are also post-transcriptionally regulated by inhibitory RNAs. Therefore, a unified database for transcriptional and post-transcriptional regulation will be highly useful for the analysis of gene expression regulation.<\/jats:p>\n          <jats:p>\n            <jats:bold>Methods<\/jats:bold>\n          <\/jats:p>\n          <jats:p>To identify putative microRNA target sites in the genome of <jats:italic>A. thaliana<\/jats:italic>, processed mature miRNAs from 243 annotated miRNA genes were used for screening with the psRNATarget web server. Positional information, target genes and the psRNATarget score for each target site were annotated to the AthaMap database. Furthermore, putative target sites for small RNAs from seven small RNA transcriptome datasets were used to determine small RNA target sites within the <jats:italic>A. thaliana<\/jats:italic> genome.<\/jats:p>\n          <jats:p>\n            <jats:bold>Results<\/jats:bold>\n          <\/jats:p>\n          <jats:p>Putative 41,965 genome wide miRNA target sites and 10,442 miRNA target genes were identified in the <jats:italic>A. thaliana<\/jats:italic> genome. Taken together with genes targeted by small RNAs from small RNA transcriptome datasets, a total of 16,600 <jats:italic>A. thaliana<\/jats:italic> genes are putatively regulated by inhibitory RNAs. A novel web-tool, \u2018MicroRNA Targets\u2019, was integrated into AthaMap which permits the identification of genes predicted to be regulated by selected miRNAs. The predicted target genes are displayed with positional information and the psRNATarget score of the target site. Furthermore, putative target sites of small RNAs from selected tissue datasets can be identified with the new \u2018Small RNA Targets\u2019 web-tool.<\/jats:p>\n          <jats:p>\n            <jats:bold>Conclusions<\/jats:bold>\n          <\/jats:p>\n          <jats:p>The integration of predicted miRNA and small RNA target sites with transcription factor binding sites will be useful for AthaMap-assisted gene expression analysis. URL: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.athamap.de\/\" ext-link-type=\"uri\">http:\/\/www.athamap.de\/<\/jats:ext-link>\n          <\/jats:p>","DOI":"10.1186\/1756-0381-5-7","type":"journal-article","created":{"date-parts":[[2012,7,16]],"date-time":"2012-07-16T14:13:58Z","timestamp":1342448038000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["\u2018MicroRNA Targets\u2019, a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana"],"prefix":"10.1186","volume":"5","author":[{"given":"Lorenz","family":"B\u00fclow","sequence":"first","affiliation":[]},{"given":"Julio C","family":"Bol\u00edvar","sequence":"additional","affiliation":[]},{"given":"Jonas","family":"Ruhe","sequence":"additional","affiliation":[]},{"given":"Yuri","family":"Brill","sequence":"additional","affiliation":[]},{"given":"Reinhard","family":"Hehl","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,7,16]]},"reference":[{"key":"61_CR1","doi-asserted-by":"publisher","first-page":"798","DOI":"10.1016\/j.semcdb.2010.03.008","volume":"21","author":"E Allen","year":"2010","unstructured":"Allen E, Howell MD: miRNAs in the biogenesis of trans-acting siRNAs in higher plants. 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