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Methods for Gene Coexpression Network Visualization and Analysis

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Transcriptomics in Health and Disease

Abstract

Gene network analysis is an important tool for studying the changes in steady states that characterize cell functional properties, the genome-environment interplay and the health-disease transitions. The integration of gene coexpression and protein interaction data is one current frontier of systems biology, leading, for instance, to the identification of unique and common drivers to disease conditions. In this chapter the fundamentals for gene coexpression network construction, visualization and analysis are revised, emphasizing its scale-free nature, the measures that express its most relevant topological features, and methods for network validation.

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Author information

Authors and Affiliations

  1. Departamento de Pediatria, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Arnaldo, 455, CEP 01246903, São Paulo, São Paulo, Brazil

    Carlos Alberto Moreira-Filho, Silvia Yumi Bando & Fernanda Bernardi Bertonha

  2. Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil

    Filipi Nascimento Silva & Luciano da Fontoura Costa

Authors
  1. Carlos Alberto Moreira-Filho
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  2. Silvia Yumi Bando
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  3. Fernanda Bernardi Bertonha
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  4. Filipi Nascimento Silva
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  5. Luciano da Fontoura Costa
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Corresponding author

Correspondence to Carlos Alberto Moreira-Filho .

Editor information

Editors and Affiliations

  1. Department of Genetics, University of São Paulo, Ribeirão Preto, São Paulo, Brazil

    Geraldo A. Passos

Supporting information (videos)

Supporting information (videos)

Video 4.1. Patients’ group CO network 3D visualization

Hubs, VIPs and high-hubs are indicated in blue, red and green, respectively. Clusters are identified by distinct colors.

Video 4.2. Control group CO network 3D visualization

Hubs, VIPs and high-hubs are indicated in blue, red and green, respectively. Clusters are identified by distinct colors.

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Moreira-Filho, C., Bando, S., Bertonha, F., Silva, F., Costa, L. (2014). Methods for Gene Coexpression Network Visualization and Analysis. In: Passos, G. (eds) Transcriptomics in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-11985-4_4

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