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Janus—a comprehensive tool investigating the two faces of transcription

Barann, Matthias ; Esser, Daniela ; Klostermeier, Ulrich C. ; Lappalainen, Tuuli ; Luzius, Anne ; Kuiper, Jan W. P. ; Ammerpohl, Ole ; Vater, Inga ; Siebert, Reiner ; Amstislavskiy, Vyacheslav ; Sudbrak, Ralf ; Lehrach, Hans ; Schreiber, Stefan ; Rosenstiel, Philip

In: Bioinformatics, 2013, vol. 29, no. 13, p. 1600-1606

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    Title
    • Janus—a comprehensive tool investigating the two faces of transcription
    Author
    • Barann, Matthias. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Esser, Daniela. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Klostermeier, Ulrich C.. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Lappalainen, Tuuli. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Luzius, Anne. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Kuiper, Jan W. P.. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Ammerpohl, Ole. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Vater, Inga. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Siebert, Reiner. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Amstislavskiy, Vyacheslav. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Sudbrak, Ralf. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Lehrach, Hans. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Schreiber, Stefan. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    • Rosenstiel, Philip. Institute for Clinical Molecular Biology (ICMB), Christian-Albrechts-University, 24105 Kiel, Germany, Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland, Institute for Human Genetics, Christian-Albrechts-University, 24105 Kiel, Germany, Max Planck Institute for Molecular Genetics and Dahlem Centre for Genome Research and Medical Systems Biology, 14195 Berlin, Germany and Department of General Internal Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
    Document Type
    • Postprint
    OAI-PMH Identifier
    • oai:doc.rero.ch:290003
    Summary
    Motivation: Protocols to generate strand-specific transcriptomes with next-generation sequencing platforms have been used by the scientific community roughly since 2008. Strand-specific reads allow for detection of antisense events and a higher resolution of expression profiles enabling extension of current transcript annotations. However, applications making use of this strandedness information are still scarce. Results: Here we present a tool (Janus), which focuses on the identification of transcriptional active regions in antisense orientation to known and novel transcribed elements of the genome. Janus can compare the antisense events of multiple samples and assigns scores to identify mutual expression of either transcript in a sense/antisense pair, which could hint to regulatory mechanisms. Janus is able to make use of single-nucleotide variant (SNV) and methylation data, if available, and reports the sense to antisense ratio of regions in the vicinity of the identified genetic and epigenetic variation. Janus interrogates positions of heterozygous SNVs to identify strand-specific allelic imbalance. Availability: Janus is written in C/C++ and freely available at http://www.ikmb.uni-kiel.de/janus/janus.html under terms of GNU General Public License, for both, Linux and Windows 64×. Although the binaries will work without additional downloads, the software depends on bamtools (https://github.com/pezmaster31/bamtools) for compilation. A detailed tutorial section is included in the first section of the supplemental material and included as brief readme.txt in the tutorial archive. Contact: m.barann@mucosa.de or p.rosenstiel@mucosa.de Supplementary information: Supplementary data are available at Bioinformatics online