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COMBO: A Computational Framework to Analyze RNA-seq and Methylation Data Through Heterogeneous Multi-layer Networks

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Complex Networks and Their Applications XI (COMPLEX NETWORKS 2016 2022)

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Abstract

Multi-layer Complex networks are commonly used for modeling and analysing biological entities. This paper presents a new computational framework called COMBO (Combining Multi Bio Omics) for generating and analyzing heterogeneous multi-layer networks. Our model uses gene expression and DNA-methylation data. The power of COMBO relies on its ability to join different omics to study the complex interplay between various components in the disease. We tested the reliability and versatility of COMBO on colon and lung adenocarcinoma cancer data obtained from the TCGA database.

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Authors and Affiliations

  1. Department of Physics and Astronomy, University of Catania, 95124, Catania, Italy

    Ilaria Cosentini

  2. Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123, Catania, Italy

    Vincenza Barresi & Daniele Filippo Condorelli

  3. Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, 95123, Catania, Italy

    Alfredo Ferro, Alfredo Pulvirenti & Salvatore Alaimo

Authors
  1. Ilaria Cosentini
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  2. Vincenza Barresi
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  3. Daniele Filippo Condorelli
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  4. Alfredo Ferro
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  5. Alfredo Pulvirenti
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  6. Salvatore Alaimo
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Corresponding author

Correspondence to Salvatore Alaimo .

Editor information

Editors and Affiliations

  1. University of Burgundy, Dijon, France

    Hocine Cherifi

  2. Dipartimento di Fisica e Chimica Emilio Segrè, Università degli Studi Palermo, Palermo, Italy

    Rosario Nunzio Mantegna

  3. Thomas J. Watson College of Engineering and Applied Science, Binghamton University, Binghamton, NY, USA

    Luis M. Rocha

  4. IUT Lumière - Université Lyon 2, University of Lyon, Bron, France

    Chantal Cherifi

  5. Dipartimento di Fisica e Chimica Emilio Segrè, Università degli Studi Palermo, Palermo, Italy

    Salvatore Miccichè

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Cosentini, I., Barresi, V., Condorelli, D.F., Ferro, A., Pulvirenti, A., Alaimo, S. (2023). COMBO: A Computational Framework to Analyze RNA-seq and Methylation Data Through Heterogeneous Multi-layer Networks. In: Cherifi, H., Mantegna, R.N., Rocha, L.M., Cherifi, C., Miccichè, S. (eds) Complex Networks and Their Applications XI. COMPLEX NETWORKS 2016 2022. Studies in Computational Intelligence, vol 1077. Springer, Cham. https://doi.org/10.1007/978-3-031-21127-0_21

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