Identifying Gene Interaction Networks

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1666)

Abstract

In this chapter, we introduce interaction networks by describing how they are generated, where they are stored, and how they are shared. We focus on publicly available interaction networks and describe a simple way of utilizing these resources. This chapter features two case studies, both of which utilize Cytoscape, an open source and user-friendly network visualization and analysis tool. In the first example, we demonstrate the basic functionalities of Cytoscape by building an interaction network from a publicly available database, analyzing its topological features, and performing gene ontology enrichment. For the second section, we constructed a network from scratch starting with an experimental gene expression dataset. From there, we implement more advanced visual annotations of the network and perform subnetwork enrichment. The methods described are applicable to larger networks that can be collected from various resources.

Key words

Interaction networks Protein–protein interactions Gene ontology Cytoscape Pathways Network Enrichment 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Systems Biology and Bioinformatics Graduate ProgramCase Western Reserve University School of MedicineClevelandUSA
  2. 2.Center for Proteomics and BioinformaticsCase Western Reserve University School of MedicineClevelandUSA
  3. 3.Department of NutritionCase Western Reserve University School of MedicineClevelandUSA
  4. 4.Department of Electrical Engineering and Computer ScienceCase Western Reserve University School of MedicineClevelandUSA

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