Selecting dissimilar genes for multi-class classification, an application in cancer subtyping

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Cai, Zhipeng ^a   Goebel, Randy ^a   Salavatipour, Mohammad R ^a   Lin, Guohui ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINARY CLASSIFICATION; BIOMARKER IDENTIFICATION; CLASSIFICATION ACCURACY; CLASSIFICATION RESULTS; GENE EXPRESSION MICROARRAY; MICROARRAY DATA ANALYSIS; MICROARRAY DATA SETS; MULTI-CLASS CLASSIFICATION;

CLASSIFICATION (OF INFORMATION); CLASSIFIERS; FORMAL LANGUAGES; GENE EXPRESSION; LEARNING SYSTEMS;

DISEASES;

ACCURACY; ARTICLE; BIOINFORMATICS; BREAST CANCER; CANCER CLASSIFICATION; CANCER GENETICS; CANCER PATIENT; CLASSIFIER; COLORECTAL CANCER; CONTROLLED STUDY; CORRELATION FUNCTION; DNA MICROARRAY; GENE CLUSTER; GENE EXPRESSION; HUMAN; INFORMATION PROCESSING; KIDNEY CANCER; LIVER CANCER; LUNG CANCER; OVARY CANCER; PROSTATE CANCER; QUANTITATIVE ANALYSIS; STATISTICAL SIGNIFICANCE; ALGORITHM; CLASSIFICATION; COMPUTER ASSISTED DIAGNOSIS; GENETIC PREDISPOSITION; GENETICS; METABOLISM; METHODOLOGY; MULTIGENE FAMILY; NEOPLASM; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

TUMOR MARKER; TUMOR PROTEIN;

ALGORITHMS; DIAGNOSIS, COMPUTER-ASSISTED; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MULTIGENE FAMILY; NEOPLASM PROTEINS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TUMOR MARKERS, BIOLOGICAL;

EID: 34547124562     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-206     Document Type: Article

References (27)

1. Alon U Barkai N Notterman DA Gish K Ybarra S Mack D Levine AJ Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays Proceedings of the National Academy of Sciences USA 1999 96 12 6745-6750 10.1073/ pnas.96.12.6745
2. Hastie T Tibshirani R Eisen MB Alizadeh A Levy R LS 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Genome Biology 2000 1 1-21 138841 11178226 10.1186/ gb-2000-1-2-research0003
3. Golub TR Slonim DK Tamayo P Huard C Gaasenbeek M Mesirov JP Coller H Loh ML Downing JR Caligiuri MA Bloomfield CD Lander ES Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring Science 1999 286 531-537 10.1126/ science.286.5439.531 10521349
4. Dudoit S Fridlyand J Speed TP Comparison of discrimination methods for the classification of tumors using gene expression data Journal of the American Statistical Association 2002 97 77-87 10.1198/016214502753479248
5. Yang K Cai Z Li J Lin GH A stable gene selection in microarray data analysis BMC Bioinformatics 2006 7 228 1524991 16643657 10.1186/ 1471-2105-7-228
6. Baldi P Long AD A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes Bioinformatics 2001 17 509-519 10.1093/bioinformatics/17.6.509 11395427
7. Cho J Lee D Park JH Lee IB New gene selection for classification of cancer subtype considering within-class variation FEBS Letters 2003 551 3-7 10.1016/S0014-5793(03)00819-6 12965195
8. Xiong M Fang X Zhao J Biomarker identification by feature wrappers Genome Research 2001 11 1878-1887 311150 11691853
9. Guyon I Weston J Barnhill S Vapnik V Gene Selection for Cancer Classification using Support Vector Machines Machine Learning 2002 46 389-422 10.1023/A:1012487302797
10. Li L Darden TA Weinberg CR Levine AJ Pedersen LG Gene assessment and sample classification for gene expression data using a genetic algorithm/ k-nearest neighbor method Combinatorial Chemistry and High Throughput Screening 2001 4 727-739
11. Lee KE Sha N Dougherty ER Vannucci M Mallick BK Gene selection: A Bayesian variable selection approach Bioinformatics 2003 19 90-97 10.1093/bioinformatics/19.1.90 12499298
12. Zhou X Liu KY Wong STC Cancer classification and prediction using logistic regression with Bayesian gene selection Journal of Biomedical Informatics 2004 37 249-259 10.1016/j.jbi.2004.07.009 15465478
13. Shevade SK Keerthi SS A simple and efficient algorithm for gene selection using sparse logistic regression Bioinformatics 2003 19 2246-2253 10.1093/bioinformatics/btg308 14630653
14. Díaz-Uriarte R Alvarez de Andres S Gene selection and classification of microarray data using random forest BMC Bioinformatics 2006 7 3 1363357 16398926 10.1186/1471-2105-7-3
15. Jaeger J Sengupta R Ruzzo WL Improved gene selection for classification of microarrays Pacific Symposium on Biocomputing 2003 8 53-64
16. Hanczar B Courtine M Benis A Hennegar C Clement K Zucker JD Improving classification of microarray data using prototype-based feature selection ACM SIGKDD Explorations Newsletter 2003 5 2 23-30 10.1145/ 980972.980977
17. Wang Y Makedon FS Ford JC Pearlman J HykGene: A hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data Bioinformatics 2005 21 1530-1537 10.1093/ bioinformatics/bti192 15585531
18. Ramaswamy S Tamayo P Rifkin R Mukherjee S Yeang CH Angelo M Ladd C Reich M Latulippe E Mesirov JP Poggio T Gerald W Loda M Lander ES Golub TR Multiclass cancer diagnosis using tumor gene expression signatures Proceedings of the National Academy of Sciences of the United States of America 2001 98 15149-15154 64998 11742071 10.1073/pnas.211566398
19. Su AI Welsh JB Sapinoso LM Kern SG Dimitrov P Lapp H Schultz PG Powell SM Moskaluk CA Frierson HF Jr Hampton GM Molecular classification of human carcinomas by use of gene expression signatures Cancer Research 2001 61 7388-7393 11606367
20. Pomeroy SL Tamayo P Gaasenbeek M Sturla LM Angelo M MEM Prediction of central nervous system embryonal tumor outcome based on gene expression Nature 2002 415 436-442 10.1038/415436a 11807556
21. Platt J Cristianini N Shawe-Taylor J Large margin DAGS for multiclass classification Advances in Neural Information Processing Systems 12 Solla SA, Leen TK, Mueller KR 2000 547-553
22. MATLAB Support Vector Machine Toolbox http://theoval.sys.uea.ac.uk/~gcc/ svm/toolbox/
23. Carcinomas dataset http://www.gnf.org/cancer/epican
24. Embryonal dataset http://www.genome.wi.mit.edu/MPR/CNS
25. Lung Carcinomas dataset http://www.genome.wi.mit.edu/MPR/lung
26. Bhattacharjee A Richards WG Staunton J Li C Monti S Vasa P Ladd C Beheshti J Bueno R Gillette M Loda M Weber G Mark EJ Lander ES Wong W Johnson BE Golub TR Sugarbaker DJ Meyerso M Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses Proceedings of National Academy of Sciences of the United States of America 2001 98 24 13790-13795 10.1073/pnas.191502998
27. All Tumor dataset http://www.genome.wi.mit.edu/MPR/gcm.html