Principles of gene microarray data analysis

Advances in Experimental Medicine and Biology

Volumn 593, Issue , 2007, Pages 19-30

  Mocellin, Simone ^a   Rossi, Carlo Riccardo ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CARCINOGENESIS; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DATA ANALYSIS; DIFFERENTIAL DISPLAY; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE MAPPING; GENE SEQUENCE; GENE TECHNOLOGY; GENOME ANALYSIS; HUMAN; INFORMATION RETRIEVAL; METHODOLOGY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; SERIAL ANALYSIS OF GENE EXPRESSION;

EID: 84934437588     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-0-387-39978-2_3     Document Type: Article

References (23)

1. Velculescu VE, Zhang L, Vogelstein B et al. Serial analysis of gene expression. Science 1995; 270(5235):484-7.
2. Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet 1999; 21(1 Suppl):33-7.
3. Schena M, Shalon D, Davis RW et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995; 270(5235):467-70.
4. Lockhart DJ, Dong H, Byrne MC et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996; 14(13): 1675-80.
5. Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat Genet 2002; 32(Suppl):490-5.
6. Dopazo J, Zanders E, Dragoni I et al. Methods and approaches in the analysis of gene expression data. J Immunol Methods 2001; 250(1-2):93-112.
7. Hess KR, Zhang W, Baggerly KA et al. Microarrays: Handling the deluge of data and extracting reliable information. Trends Biotechnol 2001; 19(11):463-8.
8. Lee ML, Kuo FC, Whitmore GA et al. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 2000; 97(18):9834-9.
9. Heller RA, Schena M, Chai A et al. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 1997; 94(6):2150-5.
10. Teague TK, Hildeman D, Kedl RM et al. Activation changes the spectrum but not the diversity of genes expressed by T cells. Proc Natl Acad Sci USA 1999; 96(22): 12691-6.
11. Claverie JM. Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet 1999; 8(10):1821-32.
12. Glynne R, Akkaraju S, Healy JI et al. How self-tolerance and the immunosuppressive drug FK506 prevent B-cell mitogenesis. Nature 2000; 403(6770):672-6.
13. Rogge L, Bianchi E, Biffi M et al. Transcript imaging of the development of human T helper cells using oligonucleotide arrays. Nat Genet 2000; 25(1):96-101.
14. Brazma A, Vilo J. Gene expression data analysis. FEBS Lett 2000; 480(1): 17-24.
15. Eisen MB, Spellman PT, Brown PO et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998; 95(25): 14863-8.
16. Nikkila J, Toronen P, Kaski S et al. Analysis and visualization of gene expression data using selforganizing maps. Neural Netw 2002; 15(8-9):953-66.
17. Crescenzi M, Giuliani A. The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data. FEBS Lett 2001; 507(1):114-8.
18. Lin K, Kuang Y, Joseph JS et al. Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: Lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002; 30(11):2599-607.
19. Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999; 286(5439):531-7.
20. Khan J, Wei JS, Ringner M et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 2001; 7(6):673-9.
21. Alizadeh AA, Eisen MB, Davis RE et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403(6769):503-11.
22. Brown MP, Grundy WN, Lin D et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 2000; 97(1):262-7.
23. Mocellin S, Provenzano M, Rossi CR et al. DNA array-based gene profiling: From surgical specimen to the molecular portrait of Cancer. Ann Surg 2005; 241(1):16-26.