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miRWalk: An online resource for prediction of microRNA binding sites

Author

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  • Carsten Sticht
  • Carolina De La Torre
  • Alisha Parveen
  • Norbert Gretz

Abstract

miRWalk is an open-source platform providing an intuitive interface that generates predicted and validated miRNA-binding sites of known genes of human, mouse, rat, dog and cow. The core of miRWalk is the miRNA target site prediction with the random-forest-based approach software TarPmiR searching the complete transcript sequence including the 5’-UTR, CDS and 3’-UTR. Moreover, it integrates results other databases with predicted and validated miRNA-target interactions. The focus is set on a modular design and extensibility as well as a fast update cycle. The database is available using Python, MySQL and HTML/Javascript Database URL: http://mirwalk.umm.uni-heidelberg.de.

Suggested Citation

  • Carsten Sticht & Carolina De La Torre & Alisha Parveen & Norbert Gretz, 2018. "miRWalk: An online resource for prediction of microRNA binding sites," PLOS ONE, Public Library of Science, vol. 13(10), pages 1-6, October.
    • Handle: RePEc:plo:pone00:0206239
    DOI: 10.1371/journal.pone.0206239
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    Cited by:

    1. Léa Maitre & Mariona Bustamante & Carles Hernández-Ferrer & Denise Thiel & Chung-Ho E. Lau & Alexandros P. Siskos & Marta Vives-Usano & Carlos Ruiz-Arenas & Dolors Pelegrí-Sisó & Oliver Robinson & Dan, 2022. "Multi-omics signatures of the human early life exposome," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    2. Junpeng Zhang & Taosheng Xu & Lin Liu & Wu Zhang & Chunwen Zhao & Sijing Li & Jiuyong Li & Nini Rao & Thuc Duy Le, 2020. "LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer," PLOS Computational Biology, Public Library of Science, vol. 16(4), pages 1-22, April.
    3. J. Tyson McDonald & JangKeun Kim & Lily Farmerie & Meghan L. Johnson & Nidia S. Trovao & Shehbeel Arif & Keith Siew & Sergey Tsoy & Yaron Bram & Jiwoon Park & Eliah Overbey & Krista Ryon & Jeffrey Hal, 2024. "Space radiation damage rescued by inhibition of key spaceflight associated miRNAs," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    4. Sarah M. Hücker & Tobias Fehlmann & Christian Werno & Kathrin Weidele & Florian Lüke & Anke Schlenska-Lange & Christoph A. Klein & Andreas Keller & Stefan Kirsch, 2021. "Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. Soumita Seth & Saurav Mallik & Atikul Islam & Tapas Bhadra & Arup Roy & Pawan Kumar Singh & Aimin Li & Zhongming Zhao, 2023. "Identifying Genetic Signatures from Single-Cell RNA Sequencing Data by Matrix Imputation and Reduced Set Gene Clustering," Mathematics, MDPI, vol. 11(20), pages 1-26, October.

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