Gene Expression Analysis via Multidimensional Scaling

Yidong Chen1, Paul S. Meltzer1

1 National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 7.11
DOI:  10.1002/0471250953.bi0711s10
Online Posting Date:  July, 2005
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Expression profiling of biological samples using microarray technologies has proven to be a powerful tool for molecular classification and biomarker identification. Visualization of similarities between biological samples from their molecular signatures is essential in forming new hypotheses. Multidimensional scaling is one of the methods that converts the structure in the similarity matrix to a simple geometrical picture: the larger the dissimilarity between two samples (evaluated through gene expression profiling), the further apart the points representing the experiments in the picture should be. In this unit, we will discuss the mathematical fundamentals of this method, along with step‐by‐step procedures that allow users to quickly obtain the results, provided that all necessary resources are ready. Examples of applying the MDS program and the interpretation of these results are also provided in this unit

Keywords: Microarray; Gene Expression Profiling; Similarity, Multidimensional Scaling (MDS); Visualization

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Table of Contents

  • Basic Protocol 1: Using the MDS Method for GENE Expression Analysis
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

Literature Cited
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   Borg, I. and Groenen, P. 1997. Modern Multidimensional Scaling: Theory and Applications. Springer, New York.
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   Green, P.E., Carmone, F.J., and Smith, S.M. 1989. Multidimensional Scaling: Concepts and Applications. Allyn and Bacon, Needham Heights, Mass.
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   Khan, J., Simon, R., Bittner, M., Chen, Y., Leighton, S.B., Pohida, T., Smith, P.D., Jiang, Y., Gooden, G.C., Trent, J.M., and Meltzer, P.S. 1998. Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. Cancer Res. 58:5009‐5113.
   Schiffman, S.S., Reynolds, M.L., and Young, F.W. 1981. Introduction to Multidimensional Scaling: Theory, Method and Applications. Academic Press, Inc., New York.
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