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International Symposium on Bioinformatics Research and Applications

ISBRA 2020: Bioinformatics Research and Applications pp 274–281Cite as

A New Network-Based Tool to Analyse Competing Endogenous RNAs

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 12304))

Abstract

Interactions between microRNA targets are defined as competing endogenous RNAs. After discovery of the repressive activity of microRNAs with different mechanisms, various experimental or computational approaches have been developed to understand the relationships among their targets. We developed a package ceRNAnetsim that provides network-based computational method as considering the expressions and interaction factors of microRNAs and their targets. By using ceRNA targets that have similar expression value as trigger on a relatively small network with 4 microRNAs and 20 gene targets, the perturbation efficiency of these ceRNAs on the network has been shown to be significantly different. However, the change was observed in the time (or iteration) to gaining steady-state of nodes on the network. So, we have provided the package which defines a user-friendly method for understanding complex ceRNA relationships, simulating the fluctuating behaviors of ceRNAs, clarifying the mechanisms of regulation and defining potentially important ceRNA elements. The ceRNAnetsim package can be found in Bioconductor software packages.

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Authors and Affiliations

  1. Chemical and Metalurgical Faculty, Bioengineering Department, Yildiz Technical University, Esenler/Istanbul, Turkey

    Selcen Ari Yuka & Alper Yilmaz

Authors
  1. Selcen Ari Yuka
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  2. Alper Yilmaz
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Corresponding author

Correspondence to Selcen Ari Yuka .

Editor information

Editors and Affiliations

  1. Department of Computer Science, Georgia State University, Atlanta, GA, USA

    Zhipeng Cai

  2. University of Connecticut, Storrs Mansfield, CT, USA

    Ion Mandoiu

  3. Florida International University, Miami, FL, USA

    Giri Narasimhan

  4. Georgia State University, Atlanta, GA, USA

    Pavel Skums

  5. University of North Texas, Denton, TX, USA

    Xuan Guo

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Yuka, S.A., Yilmaz, A. (2020). A New Network-Based Tool to Analyse Competing Endogenous RNAs. In: Cai, Z., Mandoiu, I., Narasimhan, G., Skums, P., Guo, X. (eds) Bioinformatics Research and Applications. ISBRA 2020. Lecture Notes in Computer Science(), vol 12304. Springer, Cham. https://doi.org/10.1007/978-3-030-57821-3_24

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  • DOI: https://doi.org/10.1007/978-3-030-57821-3_24

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-57820-6

  • Online ISBN: 978-3-030-57821-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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