miRPathDB

Abstract (2019)

Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged.

Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.

Authors (listed in alphabetical order)

Christina Backes
Tobias Fehlmann
Tim Kehl
Andreas Keller
Fabian Kern
Hans-Peter Lenhof
Eckard Meese
Lara Schneider
Daniel Stöckel

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How to cite

Current

miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database

Tim Kehl, Fabian Kern, Christina Backes, Tobias Fehlmann, Daniel Stöckel, Eckart Meese, Hans-Peter Lenhof, Andreas Keller. miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. Nucleic Acids Research. 2018. 10.1093/nar/gkz1022 BibTeX

@article{10.1093/nar/gkz1022,
    author = {Kehl, Tim and Kern, Fabian and Backes, Christina and Fehlmann, Tobias and Stöckel, Daniel and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
    title = "{miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database}",
    publisher = {Oxford University Press}
    journal = {Nucleic Acids Research},
    volume = {48},
    number = {D1},
    pages = {D142-D147},
    year = {2019},
    month = {11}
    doi = {10.1093/nar/gkz1022},
    url = {https://doi.org/10.1093/nar/gkz1022},
    eprint = {http://oup.prod.sis.lan/nar/article-pdf/48/D1/D142/31697924/gkz1022.pdf},
}

Additional publications

miRPathDB: a new dictionary on microRNAs and target pathways

Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckard Meese, Hans-Peter Lenhof, Andreas Keller. miRPathDB: a new dictionary on microRNAs and target pathways. Nucleic Acids Research. 2016. 10.1093/nar/gkw926 BibTeX

@article{stoeckel2016genetrail2,
  title={miRPathDB: a new dictionary on microRNAs and target pathways},
  author={Backes, Christina and Kehl, Tim and St{\"o}ckel, Daniel and Fehlmann, Tobias and Schneider, Lara and Meese, Eckard and Lenhof, Hans-Peter and Keller, Andreas},
  journal={Nucleic Acids Research},
  year={2016},
  doi={10.1093/nar/gkw926},
  publisher={Oxford University Press}
}

About miRNAs, miRNA seeds, target genes and target pathways

Tim Kehl, Christina Backes, Fabian Kern, Tobias Fehlmann, Nicole Ludwig, Eckard Meese, Hans-Peter Lenhof, Andreas Keller. About miRNAs, miRNA seeds, target genes and target pathways. Oncotarget. 2017. 10.18632/oncotarget.22363 BibTeX

@article{kehl2017mirnas,
  title={About miRNAs, miRNA seeds, target genes and target pathways},
  author={Kehl, Tim and Backes, Christina and Kern, Fabian and Fehlmann, Tobias and Ludwig, Nicole and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  journal={Oncotarget},
  volume={8},
  number={63},
  pages={107167},
  year={2017},
  publisher={Impact Journals, LLC}
}

GeneTrail2

Daniel Stöckel, Tim Kehl, Patrick Trampert, Lara Schneider, Christina Backes, Nicole Ludwig, Andreas Gerasch, Michael Kaufmann, Manfred Gessler, Norbert Graf, Eckart Meese, Andreas Keller, Hans-Peter Lenhof. Multi-omics Enrichment Analysis using the GeneTrail2 Web Service. Bioinformatics. 2016. doi: 10.1093/bioinformatics/btv770. BibTeX

@article{stoeckel2016genetrail2,
  title={Multi-omics Enrichment Analysis using the GeneTrail2 Web Service},
  author={St{\"o}ckel, Daniel and Kehl, Tim and Trampert, Patrick and Schneider, Lara and Backes, Christina and Ludwig, Nicole and Gerasch, Andreas and Kaufmann, Michael and Gessler, Manfred and Graf, Norbert and Meese, Eckart and Keller, Andreas and Lenhof, Hans-Peter},
  journal={Bioinformatics},
  year={2016},
  doi={10.1093/bioinformatics/btv770},
  publisher={Oxford University Press}
}

A dictionary on microRNAs and their putative target pathways

Christina Backes, Eckart Meese, Hans-Peter Lenhof, and Andreas Keller. A dictionary on microRNAs and their putative target pathways. Nucleic Acids Research. 2010. doi: 10.1093/nar/gkq167. BibTeX

@article{backes2010dictionary,
  title={A dictionary on microRNAs and their putative target pathways},
  author={Backes, Christina and Meese, Eckard and Lenhof, Hans-Peter and Keller, Andreas},
  journal={Nucleic Acids Research},
  year={2010},
  doi={10.1093/nar/gkq167},
  publisher={Oxford University Press}
}

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