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BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.

Xiaohui Chen1, Ming Chen, Kaida Ning

  • 1Department of Bioinformatics Zhejiang University, Hangzhou 310058, China.

Bioinformatics (Oxford, England)
|September 29, 2006
PubMed
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BNArray is a new R tool that builds gene regulatory networks from DNA microarray data using Bayesian networks. It effectively reconstructs high-confidence gene network modules, even with missing data.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Gene regulatory networks are crucial for understanding cellular processes.
  • DNA microarray data provides a rich source for inferring these networks.
  • Existing methods may struggle with missing data and identifying significant network modules.

Purpose of the Study:

  • To introduce BNArray, an R package for constructing gene regulatory networks.
  • To develop and implement an extended sub-network mining algorithm for high-confidence module identification.
  • To enable the analysis of DNA microarray data, including datasets with missing values.

Main Methods:

  • Utilized Bayesian networks for gene regulatory network construction.
  • Developed an extended sub-network mining algorithm for directed graphs.

Related Experiment Videos

  • Employed re-sampling procedures to evaluate network statistical features and identify dense, coherent sub-networks.
  • Handled DNA microarray datasets with missing data.

    • Main Results:

    • Successfully constructed gene regulatory networks from DNA microarray data.
    • Reconstructed significant sub-modules of regulatory networks with high confidence.
    • Demonstrated the capability of BNArray to manage datasets containing missing values.
    • Generated collections of candidate 1st-order network sets for robust sub-network mining.

    Conclusions:

    • BNArray is an effective systemized tool for gene regulatory network inference.
    • The extended sub-network mining algorithm enhances the identification of reliable regulatory modules.
    • BNArray provides a valuable resource for analyzing complex biological data, particularly with missing information.