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A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression

  • Faiz M. Khan
  • Mehdi Sadeghi
  • Shailendra K. Gupta
  • Olaf Wolkenhauer
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1702)

Abstract

Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches. The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks. We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling. As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions. Analysis carried out by the workflow revealed that HOXD10, BCL2, and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN, and JUNB are playing a central role. The identified key elements of each network are validated using patient survival analysis. The workflow presented here allows experimentalists to use heterogeneous data sources for the identification of diagnostic and prognostic signatures.

Key words

Integrative workflow Network-based analysis Large-scale networks Disease signatures Mathematical models 

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Faiz M. Khan
    • 1
  • Mehdi Sadeghi
    • 2
  • Shailendra K. Gupta
    • 1
    • 3
  • Olaf Wolkenhauer
    • 1
    • 3
    • 4
  1. 1.Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
  2. 2.Research Institute for Fundamental Sciences (RIFS)University of TabrizTabrizIran
  3. 3.Chhattisgarh Swami Vivekanand Technical UniversityBhilaiIndia
  4. 4.Stellenbosch Institute of Advanced Study (STIAS)Wallenberg Research Centre, Stellenbosch UniversityStellenboschSouth Africa

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