Preprocessing implementation for microarray (PRIM): An efficient method for processing cDNA microarray data

Physiological Genomics

Volumn 2001, Issue 4, 2001, Pages 183-188

  Kadota, Koji ^a,b   Miki, Rika ^a,d   Bono, Hidemasa ^a   Shimizu, Kentaro ^b   Okazaki, Yasushi ^a,c   Hayashizaki, Yoshihide ^a,c,d  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

Cluster analysis; Data processing; Expression profiling

Indexed keywords

LIGUSTRUM VULGARE;

COMPLEMENTARY DNA; MESSENGER RNA;

ANIMAL; ARTICLE; C57BL MOUSE; DNA MICROARRAY; EMBRYO; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; MOUSE; REPRODUCIBILITY; TISSUE DISTRIBUTION;

ANIMALS; DNA, COMPLEMENTARY; EMBRYO; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MICE; MICE, INBRED C57BL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; RNA, MESSENGER; TISSUE DISTRIBUTION;

EID: 0347710155     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.2001.4.3.183     Document Type: Article

References (10)

1. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson, J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, and Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403: 503-511, 2000.
2. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, and Levine AJ. 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: 6745-6750, 1999.
3. Eisen MB, Spellman PT, Brown PO, and Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868, 1998.
4. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett, DE Jr, Hartwell LH, Brown PO, and Friend SH. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 4: 1293-1301, 1999.
5. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, and Brown PO. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24: 227-235, 2000.
6. Schena M, Shalon D, Davis RW, and Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470, 1995.
7. Schuchhardt J, Beule D, Malik A, Wolski E, Eickhoff H, Lehrach H, and Herzel H. Normalization strategies for cDNA microarrays. Nucleic Acids Res 28: E47, 2000.
8. Shalon D, Smith SJ, and Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6: 639-645, 1996.
9. White KP, Rifkin SA, Hurban P, and Hogness DS. Microarray analysis of Drosophila development during metamorphosis. Science 286: 2179-2184, 1999.
10. Young RA. Biomedical discovery with DNA arrays. Cell 102: 9-15, 2000.