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Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 7292)

Abstract

Reliable inference of transcription regulatory networks is still a challenging task in the field of computational biology. Network component analysis (NCA) has become a powerful scheme to uncover the networks behind complex biological processes, especially when gene expression data is integrated with binding motif information. However, the performance of NCA is impaired by the high rate of false connections in binding motif information and the high level of noise in gene expression data. Moreover, in real applications such as cancer research, the performance of NCA in simultaneously analyzing multiple candidate transcription factors (TFs) is further limited by the small sample number of gene expression data. In this paper, we propose a novel scheme, stability-based NCA, to overcome the above-mentioned problems by addressing the inconsistency between gene expression data and motif binding information (i.e., prior network knowledge). This method introduces small perturbations on prior network knowledge and utilizes the variation of estimated TF activities to reflect the stability of TF activities. Such a scheme is less limited by the sample size and especially capable to identify condition-specific TFs and their target genes. Experiment results on both simulation data and real breast cancer data demonstrate the efficiency and robustness of the proposed method.

Keywords

  • transcription regulatory network
  • network component analysis
  • stability analysis
  • transcription factor activity
  • target genes identification

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© 2012 Springer-Verlag Berlin Heidelberg

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Chen, X., Wang, C., Shajahan, A.N., Riggins, R.B., Clarke, R., Xuan, J. (2012). Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_4

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  • DOI: https://doi.org/10.1007/978-3-642-30191-9_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30190-2

  • Online ISBN: 978-3-642-30191-9

  • eBook Packages: Computer ScienceComputer Science (R0)