title: APADB: a database for alternative polyadenylation and microRNA regulation events.
abstract: Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/.
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, GermanyPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany
authors: Sören
authors: S
authors: Müller
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Lukas
authors: L
authors: Rycak
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, GermanyPlant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany
authors: Fabian
authors: F
authors: Afonso-Grunz
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Peter
authors: P
authors: Winter
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Adam M
authors: AM
authors: Zawada
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Ewa
authors: E
authors: Damrath
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Jessica
authors: J
authors: Scheider
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Juliane
authors: J
authors: Schmäh
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Ina
authors: I
authors: Koch
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Günter
authors: G
authors: Kahl
authors: Plant Molecular Biology, Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Street 9, D-60439 Frankfurt, Germany, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, D-60438 Frankfurt, Germany, Molecular Bioinformatics Group, Faculty of Computer Science and Mathematics, Cluster of Excellence Frankfurt "Macromolecular Complexes", Institute of Computer Science, Robert-Mayer-Strasse 11-15, D-60325 Frankfurt am Main, Germany, Department of Internal Medicine IV; Saarland University Medical Center, Kirrberger Strasse, D-66421 Homburg/Saar, Germany, Experimental Neurology, Department of Neurology, Goethe University Medical School, Heinrich, Hoffmann Strasse 7, D-60528 Frankfurt am Main, Germany, Institute for Ecology, Evolution and Diversity, Aquatic Ecotoxicology, University of Frankfurt am Main, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany and Department of Pediatrics, University Hospital Schleswig-Holstein, Schwanenweg 20, D-24105 Kiel, Germany.
authors: Björn
authors: B
authors: Rotter
mesh_terms: D000818:Animals; D002645:Chickens; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D006801:Humans; D051379:Mice; D035683:MicroRNAs; D026723:Polyadenylation; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs