Random forest for gene selection and microarray data classification

Communications in Computer and Information Science

Volumn 295 CCIS, Issue , 2012, Pages 174-183

  Moorthy, Kohbalan ^a   Mohamad, Mohd Saberi ^a  

^a UNIVERSITI TEKNOLOGI MALAYSIA   (Malaysia)

Author keywords

cancer classification; classification; gene expression data; gene selection; microarray data; Random forest

Indexed keywords

CANCER CLASSIFICATION; GENE EXPRESSION DATA; GENE SELECTION; MICROARRAY DATA; RANDOM FORESTS;

DATA PROCESSING; DECISION TREES; DISEASES; GENE EXPRESSION; SET THEORY;

CLASSIFICATION (OF INFORMATION);

EID: 84865598995     PISSN: 18650929     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-32826-8_18     Document Type: Conference Paper

References (16)

1. Lee, J.W., Lee, J.B., Park, M., Song, S.H.: An extensive comparison of recent classification tools applied to microarray data. Computational Statistics & Data Analysis 48, 869-885 (2004)
2. Chin, Y.L., Deris, S.: A Study On Gene Selection And Classification Algorithms For Classification Of Microarray Gene Expression Data. Jurnal Teknologi. 43(D), 111-124 (2005)
3. Díaz-Uriarte, R., Alvarez de Andrés, S.: Gene selection and classification of microarray data using random forest. BMC Bioinformatics 2006 7(3) (2006)
4. Breiman, L.: Bagging predictors. Machine Learning 26(2), 123-140 (1996)
5. Li, T., Zhang, C., Ogihara, M.: A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics 20, 2429-2437 (2004)
6. Ramaswamy, S., Ross, K.N., Lander, E.S., Golub, T.R.: A molecular signature of metastasis in primary solid tumors. Nature Genetics 33, 49-54 (2003)
7. Pomeroy, S.L., Tamayo, P., Gaasenbeek, M., Sturla, L.M., Angelo, M., McLaughlin, M.E., Kim, J.Y., Goumnerova, L.C., Black, P.M., Lau, C., Allen, J.C., Zagzag, D., Olson, J.M., Curran, T., Wetmore, C., Biegel, J.A., Poggio, T., Mukherjee, S., Rifkin, R., Califano, A., Stolovitzky, G., Louis, D.N., Mesirov, J.P., Lander, E.S., Golub, T.R.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415, 436-442 (2002)
8. van't Veer, L.J., Dai, H., van de Vijver, M.J., He, Y.D., Hart, A.A.M., 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.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002)
9. Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D., Levine, A.J.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. 96(12), 6745-6750 (1999)
10. 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.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439), 531-537 (1999)
11. Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Losses, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell, J.I., Yang, L., Marti, G.E., Moore, T., Hudson Jr., J., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O., Staudt, L.M.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769), 503-511 (2000)
12. Ross, D.T., Scherf, U., Eisen, M.B., Perou, C.M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S.S., de Rijn, M.V., Waltham, M., Pergamenschikov, A., Lee, J.C., Lashkari, D., Shalon, D., Myers, T.G., Weinstein, J.N., Botstein, D., Brown, P.O.: Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics 24(3), 227-235 (2000)
13. Singh, D., Febbo, P.G., Ross, K., Jackson, D.G., Manola, J., Ladd, C., Tamayo, P., Renshaw, A.A., D'Amico, A.V., Richie, J.P., Lander, E.S., Loda, M., Kantoff, P.W., Golub, T.R., Sellers, W.R.: Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1, 203-209 (2002)
14. Khan, J., Wei, J.S., Ringner, M., Saal, L.H., Ladanyi, M., Westermann, F., Berthold, F., Schwab, M., Antonescu, C.R., Peterson, C., Meltzer, P.S.: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 6, 673-679 (2001)
15. Svetnik, V., Liaw, A., Tong, C., Wang, T.: Application of Breiman's random forest to modeling structure-activity relationships of pharmaceutical molecules. Multiple Classier Systems 3077, 334-343 (2004)
16. Kohavi, R.: A study of cross-validation and bootstrap for accuracy estimation and model selection. In: Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal, Quebec, Canada, August 20-25, pp. 1137-1143 (1995)