Skip to main content

Gene Selection and Sample Classification Using a Genetic Algorithm and k-Nearest Neighbor Method

  • Chapter
A Practical Approach to Microarray Data Analysis

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 54.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Alizadeh A.A., Eisen M.B., Davis R.E., Ma C., Lossos I.S., Rosenwald A., Boldrick J.C., Sabet H., Tran T., Yu X., Powell J.I., Yang L., Marti G.E., Moore T., Hudson J., Jr, Lu L., Lewis D.B., Tibshirani R., Sherlock G., Chan W.C., Greiner T.C., Weisenburger D.D., Armitage J.O., Warnke R., Staudt L.M. et al (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503–11.

    PubMed  CAS  Google Scholar 

  • Alon U., Barkai N., Notterman D.A., Gish K., Ybarra S., Mack D., Levine A.J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745–50.

    Article  PubMed  CAS  Google Scholar 

  • Baldi P., Long A.D. (2001). A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509–19.

    Article  PubMed  CAS  Google Scholar 

  • Ben-Dor A., Bruhn L., Friedman N., Nachman I., Schummer M., Yakhini Z. (2000). Tissue classification with gene expression profiles. J Comput Biol 2000; 7:559–83

    PubMed  CAS  Google Scholar 

  • Bhattacharjee A., Richards W.G., Staunton J., Li C., Monti S., Vasa P., Ladd C., Beheshti J., Bueno R., Gillette M., Loda M., Weber G., Mark E.J., Lander E.S., Wong W., Johnson B.E., Golub T.R., Sugarbaker D.J., Meyerson M. (2001). Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci USA 98:13790–5.

    Article  PubMed  CAS  Google Scholar 

  • Brazma A., Vilo J. (2000). Gene expression data analysis. FEBS Lett 480:17–24.

    Article  PubMed  CAS  Google Scholar 

  • Brown P.O., Botstein D. (1999). Exploring the new world of the genome with DNA microarrays. Nat Genet 21(1 Suppl):33–7.

    PubMed  CAS  Google Scholar 

  • Dudoit S., Yang Y.H., Callow M.J., Speed T. (2000). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Technical Report, Number 578, Department of Statistics, University of California, Berkeley, California.

    Google Scholar 

  • Dudoit S., Fridlyand J., Speed T.P. (2002). Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 97:77–87.

    Article  Google Scholar 

  • Eisen M.B., Spellman P.T., Brown P.O., Botstein D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–8.

    Article  PubMed  CAS  Google Scholar 

  • Forrest S. (1993). Genetic algorithms: principles of natural selection applied to computation. Science 261:872–8.

    PubMed  CAS  Google Scholar 

  • Furey T.S., Cristianini N., Duffy N., Bednarski D.W., Schummer M., Haussler D. (2000). Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16:906–14.

    Article  PubMed  CAS  Google Scholar 

  • Goldberg D.E. (1989) Genetic algorithms in search, optimization, and machine learning. Massachusetts: Addison-Wesley, 1989.

    Google Scholar 

  • Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., Lander E.S. (1999). Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531–7.

    Article  PubMed  CAS  Google Scholar 

  • Hedenfalk I., Duggan D., Chen Y., Radmacher M., Bittner M., Simon R., Meltzer P., Gusterson B., Esteller M., Kallioniemi O.P., Wilfond B., Borg A., Trent J. (2001). Gene-expression profiles in hereditary breast cancer. N Engl J Med 344:539–48.

    Article  PubMed  CAS  Google Scholar 

  • Holland J.H. (1975). Adaptation in Natural and Artificial Systems., Ann Arbor: University of Michigan Press.

    Google Scholar 

  • Judson R. (1997). Genetic algorthms and their use in chemistry. In Reviews in computational chemistry, Kenny B. Lipowitz and Donald B. Boyd, eds. New York: VCH publishers, Vol. 10.

    Google Scholar 

  • Li L., Darden T.A., Weinberg C.R., Levine A.J., Pedersen L.G. (2001). Gene assessment and sample classification for gene expression data using a genetic algorithm/k-nearest neighbor method. Comb Chem High Throughput Screen 4:727–39.

    PubMed  CAS  Google Scholar 

  • Li L., Weinberg C.R., Darden T.A., Pedersen L.G. (2001). Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 17:1131–42.

    PubMed  CAS  Google Scholar 

  • Li W., Xiong M. (2002). Tclass: tumor classification system based on gene expression profile. Bioinformatics 18:325–326.

    CAS  Google Scholar 

  • Lipshutz R.J., Fodor S.P., Gingeras T.R., Lockhart D.J. (1999). High density synthetic oligonucleotide arrays. Nat Genet 21(1 Suppl):20–4.

    PubMed  CAS  Google Scholar 

  • Long A.D., Mangalam H.J., Chan B.Y., Tolleri L., Hatfield G.W., Baldi P. (2001). Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem 276:19937–44.

    PubMed  CAS  Google Scholar 

  • Massart, D.L., Vandeginste B.G.M., Deming S.N., Michotte Y., Kaufman, L. (1988). Chemometrics: a textbook (Data Handling in Science and Technology, vol 2), Elsevier Science B.V: New York.

    Google Scholar 

  • Notredame C., O’Brien E.A., Higgins D.G. (1997). RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res 25:4570–80.

    Article  PubMed  CAS  Google Scholar 

  • Ooi S.L., Shoemaker D.D., Boeke J.D. (2001). A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae. Science 294:2552–6.

    Article  PubMed  CAS  Google Scholar 

  • Pan W. (2002). A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002; 18:546–54.

    Article  PubMed  CAS  Google Scholar 

  • Pedersen J.T., Moult J. (1996). Genetic algorithms for protein structure prediction. Curr Opin Struct Biol 6:227–31.

    Article  PubMed  CAS  Google Scholar 

  • Perou C.M., Sørlie T, Eisen M.B., van de Rijn M., Jeffrey S.S., Rees C.A., Pollack J.R., Ross D.T., Johnsen H., Aksien L.A., Fluge O., Pergamenschikov A., Williams C., Zhu S.X., Lonning P.E., Borresen-Dale A.L., Brown P.O., Botstein D. (2000). Molecular portraits of human breast tumours. Nature 406:747–52.

    Article  PubMed  CAS  Google Scholar 

  • Raghuraman M.K., Winzeler E.A., Collingwood D., Hunt S., Wodicka L., Conway A., Lockhart D.J., Davis R.W., Brewer B.J., Fangman W.L. (2001). Replication dynamics of the yeast genome. Science 294:115–21.

    Article  PubMed  CAS  Google Scholar 

  • Ramaswamy S., Tamayo P., Rifkin R., Mukherjee S., Yeang C.H., Angelo M., Ladd C., Reich M., Latulippe E., Mesirov J.P., Poggio T., Gerald W., Loda M., Lander E.S., Golub T.R. (2001). Multiclasscancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98:15149–54.

    Article  PubMed  CAS  Google Scholar 

  • Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., Church G.M. (1999). Systematic determination of genetic network architecture. Nat Genet 22:281–5.

    PubMed  CAS  Google Scholar 

  • Tibshirani R., Hastie T., Narasimhan B., Chu G. (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99:6567–72.

    Article  PubMed  CAS  Google Scholar 

  • Toronen P., Kolehmainen M., Wong G., Castren E. (1999). Analysis of gene expression data using self-organizing maps. FEBS Lett 451:142–6.

    PubMed  CAS  Google Scholar 

  • Tusher V.G., Tibshirani R., Chu G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–21.

    Article  PubMed  CAS  Google Scholar 

  • Vandeginste B.G.M., Massart D.L., Buydens L.M.C., De Jong S., Lewi P.J., Smeyers-Verbeke J. (1998). Handbook of Chemometrics and Qualimetrics. Vol 20B. The Netherlands: Elsevier Science.

    Google Scholar 

  • van’t Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., Peterse H.L., van der Kooy K., Marton M.J., Witteveen A.T., Schreiber G.J., Kerkhoven R.M., Roberts C., Linsley P.S., Bernards R., Friend S.H. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530–6.

    Google Scholar 

  • Virtaneva K., Wright F.A., Tanner S.M., Yuan B., Lemon W.J., Caligiuri M.A., Bloomfield C.D., de La Chapelle A., Krahe R. (2001). Expression profiling reveals fundamental biological differences in acute myeloid leukemia with isolated trisomy 8 and normal cytogenetics, Proc Natl Acad Sci USA 98:1124–9.

    Article  PubMed  CAS  Google Scholar 

  • Wyrick J.J., Young R.A. (2002). Deciphering gene expression regulatory networks. Curr Opin Genet Dev 12:130–6.

    Article  PubMed  CAS  Google Scholar 

  • Zhang H., Yu C.Y., Singer B., Xiong M. (2001). Recursive partitioning for tumor classification with gene expression microarray data. Proc Natl Acad Sci USA 98:6730–5.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Kluwer Academic Publishers

About this chapter

Cite this chapter

Li, L., Weinberg, C.R. (2003). Gene Selection and Sample Classification Using a Genetic Algorithm and k-Nearest Neighbor Method. In: Berrar, D.P., Dubitzky, W., Granzow, M. (eds) A Practical Approach to Microarray Data Analysis. Springer, Boston, MA. https://doi.org/10.1007/0-306-47815-3_12

Download citation

  • DOI: https://doi.org/10.1007/0-306-47815-3_12

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4020-7260-4

  • Online ISBN: 978-0-306-47815-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics