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Integrating Microarray Data and GRNs

  • L. KoumakisEmail author
  • G. Potamias
  • M. Tsiknakis
  • M. Zervakis
  • V. Moustakis
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1375)

Abstract

With the completion of the Human Genome Project and the emergence of high-throughput technologies, a vast amount of molecular and biological data are being produced. Two of the most important and significant data sources come from microarray gene-expression experiments and respective databanks (e,g., Gene Expression Omnibus—GEO (http://www.ncbi.nlm.nih.gov/geo)), and from molecular pathways and Gene Regulatory Networks (GRNs) stored and curated in public (e.g., Kyoto Encyclopedia of Genes and Genomes—KEGG (http://www.genome.jp/kegg/pathway.html), Reactome (http://www.reactome.org/ReactomeGWT/entrypoint.html)) as well as in commercial repositories (e.g., Ingenuity IPA (http://www.ingenuity.com/products/ipa)). The association of these two sources aims to give new insight in disease understanding and reveal new molecular targets in the treatment of specific phenotypes.

Three major research lines and respective efforts that try to utilize and combine data from both of these sources could be identified, namely: (1) de novo reconstruction of GRNs, (2) identification of Gene-signatures, and (3) identification of differentially expressed GRN functional paths (i.e., sub-GRN paths that distinguish between different phenotypes). In this chapter, we give an overview of the existing methods that support the different types of gene-expression and GRN integration with a focus on methodologies that aim to identify phenotype-discriminant GRNs or subnetworks, and we also present our methodology.

Keywords:

Microarray Gene expression Gene regulatory networks Pathways Functional pathways Bioinformatics Systems biology 

Notes

Acknowledgment

This work was supported by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement N° 270089 and by the European Union (European Social Fund—ESF) and by the European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Heracleitus II Investing in knowledge society through the European Social Fund.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • L. Koumakis
    • 1
    • 2
    Email author
  • G. Potamias
    • 2
  • M. Tsiknakis
    • 2
    • 3
  • M. Zervakis
    • 4
  • V. Moustakis
    • 1
  1. 1.Department of Production and Management EngineeringTechnical University of CreteChaniaGreece
  2. 2.Foundation for Research and Technology—Hellas (FORTH)Institute of Computer ScienceHeraklionGreece
  3. 3.Department of Applied Informatics and MultimediaTechnological Educational InstituteHeraklionGreece
  4. 4.Department of Electronic and Computer EngineeringTechnical University of CreteChaniaGreece

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