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

  • Erno Lindfors
  • Jussi Mattila
  • Peddinti V. Gopalacharyulu
  • Antti Pesonen
  • Jyrki Lötjönen
  • Matej Orešič
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 736)

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.

Keywords

Cholesterol Lipase Assure Triacylglycerol Lamin 

Notes

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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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Erno Lindfors
    • 1
  • Jussi Mattila
    • 2
  • Peddinti V. Gopalacharyulu
    • 1
  • Antti Pesonen
    • 1
  • Jyrki Lötjönen
    • 2
  • Matej Orešič
    • 1
  1. 1.VTT Technical Research Centre of FinlandEspooFinland
  2. 2.VTT Technical Research Centre of FinlandTampereFinland

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