Factor analysis of cluster-specific gene expression levels from cDNA microarrays

Computer Methods and Programs in Biomedicine

Volumn 69, Issue 3, 2002, Pages 179-188

  Peterson, Leif E ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

cDNA microarrays; Cluster analysis; Eigenanalysis; Eigenvalues; Eigenvectors; Factor analysis; Gene expression; Hierarchical agglomeration

Indexed keywords

ALGORITHMS; DNA; EIGENVALUES AND EIGENFUNCTIONS; MATRIX ALGEBRA;

GENE EXPRESSION;

GENES;

COMPLEMENTARY DNA;

ALGORITHM; ARTICLE; CANCER CELL CULTURE; CLUSTER ANALYSIS; DNA MICROARRAY; FACTORIAL ANALYSIS; GENE CLUSTER; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN;

ALGORITHMS; CLUSTER ANALYSIS; FACTOR ANALYSIS, STATISTICAL; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TUMOR CELLS, CULTURED;

EID: 0036876725     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-2607(01)00189-4     Document Type: Article

References (20)

1. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complimentary DNA microarray. Science. 270:1995;467-470.
2. DeRisi J.L., Vishwanath R., Iyer R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686.
3. Chen J.J.W., Wu R., Yang P.-C., Huang J.-Y., Sher Y.-P., Han M.-H., Kao W.-C., Lee P.-J., Chiu T.F., Chang F., Chu Y.-W., Wu C.-W., Peck K. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics. 51:1998;313-324.
4. Southern E., Mir K., Shchepinov M. Molecular interactions on microarrays. Nat. Genet. 21S:1999;5-9.
5. Scherf U., Ross D.T., Waltham M., Smith L.H., Lee J.K., Tanabe L., Kohn K.W., Reinhold W.C., Myers T.G., Andrews D.T., Scudiero D.A., Eisen M.B., Sausville E.A., Pommier Y., Botstein D., Brown P.O., Weinstein J.N. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24:2000;236-244.
6. 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., Akslen L.A., Fluge Ø., Pergamenschikov A., Williams C., Zhu S.X., Lønning P., Børreson-Dale A.-L., Brown P.O., Botstein D. Molecular portraits of human breast tumours. Nature. 406:2000;747-752.
7. Lehman T.A., Haffty B.G., Carbone C.J., Bishop L.R., Gumbs A.A., Krishnan S., Shields P.G., Modali R., Turner B.C. Elevated frequency and functional activity of a specific germ-line p53 intron mutation in familial breast cancer. Cancer Res. 60:2000;1062-1069.
8. Ono K., Tanaka T., Tsunoda T., Kitahara O., Kihara C., Okamoto A., Ochiai K., Takagi T., Nakamura Y. Identification by cDNA microarray of genes involved in ovarian carcinogenesis. Cancer Res. 60:2000;5007-5011.
9. Richter J., Wagner U., Kononen J., Fijan A., Bruderer J., Schmid U., Ackermann D., Maurer R., Alund G., Knonagel H., Rist M., Wilber K., Anabitarte M., Hering F., Hardmeier T., Schonenberger A., Flury R., Jager P., Fehr J.L., Schraml P., Moch H., Mihatsch M.J., Gasser T., Kallioniemi O.P., Sauter G. High-throughput tissue microarray analysis of cyclin E gene amplification and overexpression in urinary bladder cancer. Am. J. Pathol. 157:2000;787-794.
10. 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. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 403:2000;503-511.
11. Ross D.T., Scherf U., Eisen M.B., Perou C.M., Rees C., Spellman P., Iyer V., Jeffrey S.S., Van de Rijn M., 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. Nat. Genet. 24:2000;227-235.
12. Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 2:1998;65-73.
13. Ferea T.L., Botstein D., Brown P.O., Rosenzweig R.F. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. 96:1999;9721-9726.
14. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell. 9:1998;3273-3297.
15. Iyer V.R., Eisen M.B., Ross D.T., Schuler G., Moore T., Lee J.C.F., Trent J.M., Staudt L.M., Hudson J. Jr., Boguski M.S., Lashkari D., Shalon D., Botstein D., Brown P.O. The transcriptional program in the response of human fibroblasts to serum. Science. 283:1999;83-87.
16. Whitney L.W., Becker K.G., Tresser N.J., Caballero-Ramos C.I., Munson P.J., Prabhu V.V., Trent J.M., McFarland H.F., Biddison W.E. Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays. Ann. Neurol. 46:1999;425-428.
17. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95:1998;14 863-14 868.
18. Khan J., Saal L.H., Bittner M.L., Chen Y., Trent J.M., Meltzer P.S. Expression profiling in cancer using cDNA microarrays. Electrophoresis. 20:1999;223-229.
19. van Hal N.L.W., Vosrt O., van Houwelingen A.M.M.L., Kok E.J., Piejnenburg A., Aharoni A., van Tunen A.J., Keijer J. The application of DNA microarrays on gene expression analysis. J. Biotech. 78:2000;271-280.
20. H.H. Harman, Objective Orthogonal Multiple-Factor Solutions, Chap. 13., In: Modern Factor Analysis, University of Chicago Press (1967).