Van Eyk, Dunn - Proteomic and Genomic Analysis of Cardiovascular Disease - 2003 (522919), страница 10
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1.3. The work is supported by the NHLBI Programs for Genomic Applications, U01 HL66582.23241 Microarray Expression Profiling in Cardiovascular Disease1.5References1234567891011Cho RJ, Campbell MJ, Winzeler EA,Steinmetz L, et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell. 1998; 2(1):65–73.Shipp MA, Ross KN, Tamayo P, WengAP, et al. Diffuse large B-cell lymphomaoutcome prediction by gene-expressionprofiling and supervised machine learning. Nat.
Med. 2002; 8(1):68–74.Lander ES, Linton LM, Birren B, Nusbaum C, et al. Initial sequencing andanalysis of the human genome. Nature2001; 409(6822):860–921.Adams MD, Kelley JM, Gocayne JD,Dubnick M, et al. Complementary DNAsequencing: expressed sequence tags andhuman genome project. Science 1991;252(5013):1651–1656.Schena M, Shalon D, Davis RW,Brown PO. Quantitative monitoring ofgene expression patterns with a complementary DNA microarray. Science 1995;270(5235):467–470.Velculescu VE, Zhang L, VogelsteinB, Kinzler KW.
Serial analysis of geneexpression. Science 1995; 270(5235):484–487.Lockhart DJ, Dong H, Byrne MC, Follettie MT, et al. Expression monitoringby hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 1996;14(13):1675–1680.Brenner S, Johnson M, Bridgham J,Golda G, et al. Gene expression analysisby massively parallel signature sequencing (MPSS) on microbead arrays. Nat.Biotechnol.
2000; 18(6):630–634.Sutcliffe JG, Foye PE, Erlander MG,Hilbush BS, et al. TOGA: an automatedparsing technology for analyzing expression of nearly all genes. Proc. Natl. Acad.Sci. USA. 2000; 97(5):1976–1981.Kane MD, Jatkoe TA, Stumpf CR, Lu J,et al. Assessment of the sensitivity andspecificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 2000;28(22):4552–4557.Ohyama H, Zhang X, Kohno Y, Alevizos I, et al.
Laser capture microdissection-generated target sample for high-1213141516171819202122density oligonucleotide array hybridization. Biotechniques 2000; 29(3):530–536.Baugh LR, Hill AA, Brown EL, Hunter CP. Quantitative analysis of mRNAamplification by in vitro transcription.Nucleic Acids Res. 2001; 29(5):E29.Soloviev M. EuroBiochips: spot the difference! Drug Discov. Today 2001;6(15):775–777.Gossen M, Bujard H. Tight control ofgene expression in mammalian cells bytetracycline-responsive promoters.
Proc.Natl. Acad. Sci. USA. 1992; 89(12):5547–5551.Li C, Wong WH. Model-based analysisof oligonucleotide arrays: expression index computation and outlier detection.Proc. Natl. Acad. Sci. USA. 2001;98(1):31–36.Chudin E, Walker R, Kosaka A, WuSX, et al. Assessment of the relationshipbetween signal intensities and transcriptconcentration for Affymetrix GeneChip(R) arrays. Genome Biol. 2002; 3(1):Research 0005.1–0005.10.Quackenbush J. Computational analysisof microarray data. Nat. Rev.
Genet. 2001;2(6):418–427.Hedenfalk I, Duggan D, Chen Y, Radmacher M, et al. Gene-expression profiles in hereditary breast cancer. N. Engl.J. Med. 2001; 344(8):539–548.Chen Y, Dougherty ER, Bittner ML.Ratio-based decisions and the quantitative analysis of cDNA microarray images.J. Biomed. Opt. 1997; 2:364–374.Cleveland WS, Devlin SJ. Locallyweighted regression: an approach to regression analysis by local fitting. J. Am.Stat. Assoc.
1988; 83:596–610.Ramdas L, Coombes KR, Baggerly K,Abruzzo L, et al. Sources of nonlinearityin cDNA microarray expression measurements. Genome Biol. 2001; 2(11).Tseng GC, Oh MK, Rohlin L, Liao JC,et al. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res.2001; 29(12):2549–2557.1.5 References2324252627282930313233Depre C, Tomlinson JE, Kudej RK,Gaussin V, et al. Gene program for cardiac cell survival induced by transientischemia in conscious pigs. Proc. Natl.Acad.
Sci. USA. 2001; 98(16):9336–9341.Yang J, Moravec CS, Sussman MA, DiPaola NR, et al. Decreased SLIM1 expression and increased gelsolin expression in failing human hearts measuredby high-density oligonucleotide arrays.Circulation 2000;1 02(25):3046–3052.Jin H, Yang R, Awad TA, Wang F, et al.Effects of early angiotensin-convertingenzyme inhibition on cardiac gene expression after acute myocardial infarction.
Circulation 2001; 103(5):736–742.Golub TR, Slonim DK, Tamayo P,Huard C, et al. Molecular classificationof cancer: class discovery and class prediction by gene expression monitoring.Science 1999; 286(5439):531–537.Quinlan J. C4.5: programs for machinelearning.
San Mateo, Calif.: MorganKaufmann; 1992.Rumelhart D, McClelland J, University of California SDPRG. Parallel distributed processing : explorations in the microstructure of cognition. Cambridge,Mass.: MIT Press; 1986.Furey TS, Cristianini N, Duffy N,Bednarski DW, et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 2000;16(10):906–914.Brown MP, Grundy WN, Lin D, Cristianini N, et al.
Knowledge-based analysis of microarray gene expression data byusing support vector machines. Proc. Natl.Acad. Sci. USA. 2000; 97(1):262–267.Chow ML, Moler EJ, Mian IS. Identifying marker genes in transcription profiling data using a mixture of feature relevance experts. Physiol. Genomics 2001;5(2):99–111.Alter O, Brown PO, Botstein D. Singular value decomposition for genomewide expression data processing andmodeling. Proc.
Natl. Acad. Sci. USA.2000; 97(18):10101–10106.Raychaudhuri S, Stuart JM, AltmanRB. Principal components analysis tosummarize microarray experiments: ap-3435363738394041424344plication to sporulation time series. Pac.Symp. Biocomput. 2000, 455–466.Fiehn O, Kopka J, Dormann P, Altmann T, et al. Metabolite profiling forplant functional genomics.
Nat. Biotechnol. 2000; 18(11):1157–1161.Wen X, Fuhrman S, Michaels GS,Carr DB, et al. Large-scale temporalgene expression mapping of central nervous system development. Proc. Natl.Acad. Sci. USA. 1998; 95(1):334–339.Hilsenbeck SG, Friedrichs WE,Schiff R, O’Connell P, et al.
Statisticalanalysis of array expression data as applied to the problem of tamoxifen resistance. J. Natl. Cancer Inst. 1999;91(5):453–459.Ben-Dor A, Bruhn L, Friedman N,Nachman I, et al. Tissue classificationwith gene expression profiles. J. Comput.Biol. 2000; 7(3–4):559–583.Tamayo P, Slonim D, Mesirov J, ZhuQ, et al. Interpreting patterns of gene expression with self-organizing maps:Methods and application to hematopoietic differentiation. Proc. Natl.
Acad. Sci.USA. 1999; 96(6):2907–2912.Toronen P, Kolehmainen M, Wong G,Castren E. Analysis of gene expressiondata using self-organizing maps. FEBSLett. 1999; 451(2):142–146.Eisen MB, Spellman PT, Brown PO,Botstein D. Cluster analysis and displayof genome-wide expression patterns.Proc. Natl. Acad. Sci. USA. 1998;95(25):14863–14868.Ross DT, Scherf U, Eisen MB, PerouCM, et al. Systematic variation in geneexpression patterns in human cancer celllines. Nat. Genet.
2000; 24(3):227–235.Liang S, Fuhrman S, Somogyi R. Reveal, a general reverse engineering algorithm for inference of genetic networkarchitectures. Pac. Symp. Biocomput.1998, 18–29.Wuensche A. Genomic regulation modeled as a network with basins of attraction. Pac. Symp. Biocomput. 1998, 89–102.Szallasi Z, Liang S. Modeling the normal and neoplastic cell cycle with “realistic Boolean genetic networks”: their application for understanding carcinogen-25261 Microarray Expression Profiling in Cardiovascular Disease45464748495051525354esis and assessing therapeutic strategies.Pac.
Symp. Biocomput. 1998, 66–76.Friedman N, Linial M, Nachman I,Pe’er D. Using Bayesian networks toanalyze expression data. J. Comput. Biol.2000; 7(3–4):601–620.Butte A, Kohane I. UnsupervisedKnowledge Discovery in Medical Databases Using Relevance Networks. In:Lorenzi N, editor. Fall Symposium,American Medical Informatics Association; 1999; Washington, DC: Hanley andBelfus; 1999, p. 711–715.Butte AJ, Kohane IS. Mutual information relevance networks: functional genomic clustering using pairwise entropymeasurements.
Pac. Symp. Biocomput.2000, 418–429.Butte AJ, Tamayo P, Slonim D, GolubTR, et al. Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proc. Natl. Acad. Sci.USA. 2000; 97(22):12182–12186.Lele S, Richtsmeier JT. Euclidean distance matrix analysis: confidence intervals for form and growth differences.Am. J. Phys.
Anthropol. 1995; 98(1):73–86.Hartigan JA, Wong MA. A K-MeansClustering Algorithm. Applied Statistics1979; 28:100–108.Aronow BJ, Toyokawa T, Canning A,Haghighi K, et al. Divergent transcriptional responses to independent geneticcauses of cardiac hypertrophy. Physiol.Genomics 2001; 6(1):19–28.Kohonen T. Physiolocigal interpretationof the self-organizing map algorithm.Neural Networks 1993; 6(7):895–905.Tamayo P, Slonim D, Mesirov J, ZhuQ, et al.
Interpreting patterns of gene expression with self-organizing maps:methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci.USA. 1999; 96(6):2907–2912.Sherlock G, Hernandez-Boussard T,Kasarskis A, Binkley G, et al. The Stanford Microarray Database. Nucleic AcidsRes. 2001; 29(1):152–155.55565758596061626364Lyn D, Liu X, Bennett NA, Emmett NL.Gene expression profile in mouse myocardium after ischemia. Physiol. Genomics2000; 2(3):93–100.Sehl PD, Tai JT, Hillan KJ, Brown LA,et al.
Application of cDNA microarrays indetermining molecular phenotype in cardiac growth, development, and responseto injury. Circulation 2000; 101(16):1990–1999.Stanton LW, Garrard LJ, Damm D,Garrick BL, et al. Altered patterns of geneexpression in response to myocardial infarction. Circ. Res. 2000; 86(9):939–945.Friddle CJ, Koga T, Rubin EM, Bristow J. Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy.
Proc. Natl. Acad. Sci. USA. 2000;97(12):6745–6750.Liu T, Lai H, Wu W, Chinn S, WangPH. Developing a strategy to define theeffects of insulin-like growth factor-1 ongene expression profile in cardiomyocytes. Circ. Res. 2001; 88(12):1231–1238.Barrans JD, Stamatiou D, Liew C. Construction of a human cardiovascularcDNA microarray: portrait of the failingheart. Biochem. Biophys. Res. Commun.2001; 280(4):964–969.Taylor LA, Carthy CM, Yang D, SaadK, et al.
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