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Supplemental Information for:

Molecular Classification of Cutaneous Malignant
Melanoma by Gene Expression Profiling

M. Bittner1*, P. Meltzer1*, Y. Chen1, Y. Jiang1, E. Seftor2, M. Hendrix2, M. Radmacher3, R. Simon3, Z. Yakhini4, A. Ben-Dor4, E. Dougherty5, E. Wang6, F. Marincola6, C. Gooden1, J. Lueders1, A. Glatfelter1, P. Pollock7, E. Gillanders1, D. Leja1, K. Dietrich1, C. 8, M. Berens8, D. Alberts9, V. Sondak10, N. Hayward7, and J. Trent1


1 Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892 2 Department of Anatomy and Cell Biology, University of Iowa Cancer Center, Iowa City, Iowa 52242-1109 3 National Cancer Institute, DCTDC, NIH, Bethesda, Maryland 20852 4 Department of Computer Science & Engineering, Hewlett-Packard Laboratories, Haifa 32000 Israel 5 Department of Electrical Engineering, Texas A & M University, College Station, Texas 77843 6 National Cancer Institute, Department of Surgery, NIH, Bethesda, Maryland 20850 7 Queensland Institute of Medical Research, Herston, 4029, Queensland, Australia 8Neuro-Oncology Laboratory, Barrow Neurological Institute Phoenix, AZ 85013-4496 9 Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724 10 Department of Surgery, The University of Michigan, Ann Arbor, Michigan 48109

*Authors participated equally/§corresponding author J. Trent (jtrent@nhgri.nih.gov)

 
  1. Three-dimensional Animation of the Multidimensional Scaling (MDS) Graphic Displayed in Figure 1b


  2. Statistical Methods for Clustering of Gene Expression Data and Validation of Cluster Predictions

  3. Statistical Analysis of Clinical and Culture Characteristics of Melanoma Clusters

  4. Gene List -- Cutaneous Melanoma

  5. Gene List – Uveal Melanoma

  6. Weighted Gene List

  7. Table 2: Mutational Changes for p16 identified by Direct Sequencing

  8. Table 3: Summary of Clinical Information of Melanoma Cases by Cluster Designation

  9. Table 4: Quality Control Genotyping

  10. Expanded Microarray Methodology

  11. Figures and Tables

    Figure 1. Clustering results of melanoma samples
    Figure 2. Generation of weighted gene list.
    Figure 3. Using weighted gene list to interrogate gene cluster results.
    Figure 4. Bioassays associated with cluster prediction.
       
    Table 1. Summary of Melanoma Cases by Cluster Designation.
    Table 2. Mutational Changes for p16 identified by Direct Sequencing.
    Table 3. Summary of Clinical Information of Melanoma Cases by Cluster Designation.

  12. Acknowledgements






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