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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 8, Issue 2

Issues

Integrating Protein-Protein Interaction Networks with Gene- Gene Co-Expression Networks improves Gene Signatures for Classifying Breast Cancer Metastasis

Erik van den Akker
  • Corresponding author
  • Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands Netherlands
  • The Delft Bioinformatics Lab, Delft University of Technology, Delft, Netherlands
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Bas Verbruggen / Bas Heijmans
  • Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands Netherlands
  • Netherlands Consortium of Healthy Ageing, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Marian Beekman
  • Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands Netherlands
  • Netherlands Consortium of Healthy Ageing, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Joost Kok
  • Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands Netherlands
  • Algorithms, Leiden Institute of Advanced Computer Science, University Leiden, Leiden, The Netherlands Netherlands
  • Netherlands Bioinformatics Centre, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Eline Slagboom
  • Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands Netherlands
  • Netherlands Consortium of Healthy Ageing, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Marcel Reinders
  • The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands Netherlands
  • Netherlands Bioinformatics Centre, Netherlands
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2011-188

Summary

Multiple studies have illustrated that gene expression profiling of primary breast cancers throughout the final stages of tumor development can provide valuable markers for risk prediction of metastasis and disease sub typing. However, the identification of a biologically interpretable and universally shared set of markers proved to be difficult. Here, we propose a method for de novo grouping of genes by dissecting the proteinprotein interaction network into disjoint sub networks using pair wise gene expression correlation measures. We show that the obtained sub networks are functionally coherent and are consistently identified when applied on a compendium composed of six different breast cancer studies. Application of the proposed method using different integration approaches underlines the robustness of the identified sub network related to cell cycle and identifies putative new sub network markers for metastasis related to cell-cell adhesion, the proteasome complex and JUN-FOS signalling. Although gene selection with the proposed method does not directly improve upon previously reported cross study classification performances, it shows great promises for applications in data integration and result interpretation.

About the article

Published Online: 2016-10-18

Published in Print: 2011-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 8, Issue 2, Pages 222–238, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2011-188.

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© 2011 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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