Nonnegative Network Component Analysis by Linear Programming for Gene Regulatory Network Reconstruction

  • Chunqi Chang
  • Zhi Ding
  • Yeung Sam Hung
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5441)


We consider a systems biology problem of reconstructing gene regulatory network from time-course gene expression microarray data, a special blind source separation problem for which conventional methods cannot be applied. Network component analysis (NCA), which makes use of the structural information of the mixing matrix, is a tailored method for this specific blind source separation problem. In this paper, a new NCA method called nonnegative NCA (nnNCA) is proposed to take into account of the non-negativity constraint on the mixing matrix that is based on a reasonable biological assumption. The nnNCA problem is formulated as a linear programming problem which can be solved effectively. Simulation results on spectroscopy data and experimental results on time-course microarray data of yeast cell cycle demonstrate the effectiveness and anti-noise robustness of the proposed nnNCA method.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Chunqi Chang
    • 1
  • Zhi Ding
    • 2
  • Yeung Sam Hung
    • 1
  1. 1.Department of Electrical and Electronic EngineeringThe University of Hong KongHong Kong
  2. 2.Department of Electrical and Computer EngineeringUniversity of CaliforniaDavisUSA

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