Selection and validation of differentially expressed genes in head and neck cancer (original) (raw)

Abstract

We applied a robust combinatorial (multi-test) approach to microarray data to identify genes consistently up- or down-regulated in head and neck squamous cell carcinoma (HNSCC). RNA was extracted from 22 paired samples of HNSCC and normal tissue from the same donors and hybridized to the Affymetrix U95A chip. Forty-two differentially expressed probe sets (representing 38 genes and one expressed sequence tag) satisfied all statistical tests of significance and were selected for further validation. Selected probe sets were validated by hierarchical clustering, multiple probe set concordance, and target-subunit agreement. In addition, real-time PCR analysis of 8 representative (randomly selected from 38) genes performed on both microarray-tested and independently obtained samples correlated well with the microarray data. The genes identified and validated by this method were in comparatively good agreement with other rigorous HNSCC microarray studies. From this study, we conclude that combinatorial analysis of microarray data is a promising technique for identifying differentially expressed genes with few false positives.

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Authors and Affiliations

  1. Department of Otolaryngology, Division of Head and Neck Surgery, New York School of Medicine, 411 Rusk Research Building, 400E, 34th Street, 10016, New York, NY, USA
    M. A. Kuriakose, Z. M. He, A. G. Sikora, M. D. Delacure & F. A. Chen
  2. Department of Oral and Maxillofacial Surgery, Affiliated Ninth People’s Hospital, School of Stomatology, Shanghai Second Medical University, 200011, Shanghai, P. R. China
    W. T. Chen, P. Zhang, Z. Y. Zhang & W. L. Qiu
  3. Department of Computer and Information Sciences, Fordham University, 10023, New York, NY, USA
    D. F. Hsu & C. McMunn-Coffran
  4. Department of Research Computing, New York University School of Medicine, 10016, New York, NY, USA
    S. M. Brown
  5. Amrita Institute of Medical Science, Cochin, India
    E. M. Elango

Authors

  1. M. A. Kuriakose
  2. W. T. Chen
  3. Z. M. He
  4. A. G. Sikora
  5. P. Zhang
  6. Z. Y. Zhang
  7. W. L. Qiu
  8. D. F. Hsu
  9. C. McMunn-Coffran
  10. S. M. Brown
  11. E. M. Elango
  12. M. D. Delacure
  13. F. A. Chen

Corresponding author

Correspondence toF. A. Chen.

Additional information

Received 12 February 2004; received after revision 22 March 2004; accepted 14 April 2004

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Kuriakose, M.A., Chen, W.T., He, Z.M. et al. Selection and validation of differentially expressed genes in head and neck cancer.CMLS, Cell. Mol. Life Sci. 61, 1372–1383 (2004). https://doi.org/10.1007/s00018-004-4069-0

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