Extracting Global Structure from Gene Expression Profiles

  • Charless Fowlkes
  • Qun Shan
  • Serge Belongie
  • Jitendra Malik


We have developed a program, GENECUT, for analyzing datasets from gene expression profiling. GENECUT is based on a pairwise clustering method known as Normalized Cut [Shi and Malik, 1997]. GENECUT extracts global structures by progressively partitioning datasets into well-balanced groups, performing an intuitive k-way partitioning at each stage in contrast to commonly used 2-way partitioning schemes. By making use of the Nyström approximation, it is possible to perform clustering on very large genomic datasets.

Key words

gene expression profiles clustering analysis spectral partitioning 


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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Charless Fowlkes
    • 1
  • Qun Shan
    • 2
  • Serge Belongie
    • 3
  • Jitendra Malik
    • 1
  1. 1.Departments of Computer ScienceUniversity of California at BerkeleyUSA
  2. 2.Molecular Cell BiologyUniversity of California at BerkeleyUSA
  3. 3.Department of Computer Science and EngineeringUniversity of California at San DiegoUSA

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