About

Abstract

For the analysis of miRNAs targeting genes and pathways several tools exist. We previously presented a dictionary on single miRNAs and their putative target pathways. Since that time, the number of miRNAs has tripled and the knowledge on miRNAs and targets, especially experimentally validated ones, has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs targeting pathways.

Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/. With the database we aim to augment available target pathway web-servers by providing researches easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific the regulations are. The database contains a large number of miRNAs (2,599 human miRNAs), different miRNA target sets (14,773 experimentally validated target genes as well as 19281 predicted targets genes) and a broad selection of functional biochemical categories (280 KEGG-, 296 WikiPathways-, 310 BioCarta-, 617 SMPDB-, 221 PID-, 1,300 Reactome pathways, 6,169 biological processes, 1,550 molecular functions, and 758 cellular components from Gene Ontology, and 806 cytogenetic bands, totaling 12,875 categories). In addition to H. sapiens, also M. musculus data are stored and can be compared to human target pathways.

Authors

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

*The first two authors contributed equally to the study and are listed in alphabetic order

Contact

If you have any questions or suggestions for improving the miRNA Pathway Dictionary do not hesitate to contact us.

Options

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  • Contact the developers directly
  • Regular mail
    • Chair for Bioinformatics Saarbrücken
    • Building E2 1
    • Saarland Informatics Campus
    • Saarland University
    • P.O. box 151150
    • D - 66041 Saarbrücken

How to cite

Current

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}
}

Additional publications

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}
}