Constructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants

  • Tomás C. Moyano
  • Elena A. Vidal
  • Orlando Contreras-López
  • Rodrigo A. Gutiérrez
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)


Technological advances in the last decade have enabled biologists to produce increasing amounts of information for the transcriptome, proteome, interactome, and other -omics data sets in many model organisms. A major challenge is integration and biological interpretation of these massive data sets in order to generate testable hypotheses about gene regulatory networks or molecular mechanisms that govern system behaviors. Constructing gene networks requires bioinformatics skills to adequately manage, integrate, analyze and productively use the data to generate biological insights. In this chapter, we provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape platforms. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.

Key words

Gene networks Bioinformatics Interactions Networks generation Gene expression Correlation Cytoscape 



Research in our group is funded by the International Early Career Scientist program from Howard Hughes Medical Institute, Fondo de Desarrollo de Areas Prioritarias (FONDAP) Center for Genome Regulation (15090007), Millennium Nucleus Center for Plant Functional Genomics (P10-062-F), Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT) 1141097 and 11121225. T.C.M. is funded by CONICYT doctoral fellowship 21110366.


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Tomás C. Moyano
    • 1
  • Elena A. Vidal
    • 1
  • Orlando Contreras-López
    • 1
  • Rodrigo A. Gutiérrez
    • 1
  1. 1.Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Nucleus for Plant Functional GenomicsPontificia Universidad Católica de ChileSantiagoChile

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