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Heterogeneous Biological Network Visualization System: Case Study in Context of Medical Image Data

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Advances in Systems Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 736))

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Abstract

We have developed a system called megNet for integrating and visualizing heterogeneous biological data in order to enable modeling biological phenomena using a systems approach. Herein we describe megNet, including a recently developed user interface for visualizing biological networks in three dimensions and a web user interface for taking input parameters from the user, and an in-house text mining system that utilizes an existing knowledge base. We demonstrate the software with a case study in which we integrate lipidomics data acquired in-house with interaction data from external databases, and then find novel interactions that could possibly explain our previous associations between biological data and medical images. The flexibility of megNet assures that the tool can be applied in diverse applications, from target discovery in medical applications to metabolic engineering in industrial biotechnology.

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Acknowledgments

We thank Dr. Laxman Yetukuri for technical assistance in mapping lipidomics data to metabolic pathways. The project was supported by the research program “White Biotechnology – Green Chemistry” (Academy of Finland; Finnish Centre of Excellence programme, 2008–2013, Decision number 118573), by the EU project MITIN (HEALTH-F4–2008–223450), by the National Graduate School in Informational and Structural Biology (ISB), and by the TRANSCENDO project of the Tekes MASI Program.

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Authors and Affiliations

  1. VTT Technical Research Centre of Finland, Tietotie 2, Espoo, Finland

    Erno Lindfors, Peddinti V. Gopalacharyulu, Antti Pesonen & Matej Orešič

  2. VTT Technical Research Centre of Finland, Sinitaival 6, Tampere, Finland

    Jussi Mattila & Jyrki Lötjönen

Authors
  1. Erno Lindfors
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  2. Jussi Mattila
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  3. Peddinti V. Gopalacharyulu
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  4. Antti Pesonen
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  5. Jyrki Lötjönen
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  6. Matej Orešič
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Corresponding author

Correspondence to Erno Lindfors .

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Editors and Affiliations

  1. School of Informatics, University of Edinburgh, Crichton Street 10, Edinburgh, EH89AB, UK

    Igor I. Goryanin

  2. School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh, EH93JR, UK

    Andrew B. Goryachev

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Lindfors, E., Mattila, J., Gopalacharyulu, P.V., Pesonen, A., Lötjönen, J., Orešič, M. (2012). Heterogeneous Biological Network Visualization System: Case Study in Context of Medical Image Data. In: Goryanin, I.I., Goryachev, A.B. (eds) Advances in Systems Biology. Advances in Experimental Medicine and Biology, vol 736. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7210-1_5

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