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An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer

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Pseudogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2324))

Abstract

Pools of RNA molecules can act as competing endogenous RNAs (ceRNAs) and indirectly alter their expression levels by competitively binding shared microRNAs. This ceRNA cross talk yields an additional posttranscriptional regulatory layer, which plays key roles in both physiological and pathological processes. MicroRNAs can act as decoys by binding multiple RNAs, as well as RNAs can act as ceRNAs by competing for binding multiple microRNAs, leading to many cross talk interactions that could favor significant large-scale effects in spite of the weakness of single interactions. Identifying and studying these extended ceRNA interaction networks could provide a global view of the fine-tuning gene regulation in a wide range of biological processes and tumor progressions. In this chapter, we review current progress of predicting ceRNA cross talk, by summarizing the most up-to-date databases, which collect computationally predicted and/or experimentally validated miRNA–target and ceRNA–ceRNA interactions, as well as the widespread computational methods for discovering and modeling possible evidences of ceRNA–ceRNA interaction networks. These methods can be grouped in two categories: statistics-based methods exploit multivariate analysis to build ceRNA networks, by considering the miRNA expression levels when evaluating miRNA sponging relationships; mathematical methods build deterministic or stochastic models to analyze and predict the behavior of ceRNA cross talk.

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Authors and Affiliations

  1. Institute for Systems Analysis and Computer Science Antonio Ruberti, National Research Council, Rome, Italy

    Federica Conte, Giulia Fiscon, Pasquale Sibilio & Paola Paci

  2. Fondazione per la Medicina Personalizzata (FMP), Genova, Italy

    Giulia Fiscon

  3. Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy

    Pasquale Sibilio

  4. Biology and Biotechnology Department Charles Darwin (BBCD), Sapienza University of Rome, Rome, Italy

    Valerio Licursi

  5. Department of Computer, Control, and Management Engineering Antonio Ruberti (DIAG), Sapienza University of Rome, Rome, Italy

    Paola Paci

Authors
  1. Federica Conte
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  2. Giulia Fiscon
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  3. Pasquale Sibilio
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  4. Valerio Licursi
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  5. Paola Paci
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Corresponding author

Correspondence to Paola Paci .

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Editors and Affiliations

  1. Oncogenomics Unit, Core Research Laboratory, ISPRO, Institute of Clinical Physiology (IFC), CNR, Pisa, Italy

    Laura Poliseno

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Conte, F., Fiscon, G., Sibilio, P., Licursi, V., Paci, P. (2021). An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer. In: Poliseno, L. (eds) Pseudogenes. Methods in Molecular Biology, vol 2324. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1503-4_10

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  • DOI: https://doi.org/10.1007/978-1-0716-1503-4_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1502-7

  • Online ISBN: 978-1-0716-1503-4

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