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Volumn 22, Issue 1, 2008, Pages 7-16

From single gene to integrative molecular concept maps: Pitfalls and potentials of microarray technology

Author keywords

Enrichment analysis; Feature selection; Gene profiling; High throughput technology

Indexed keywords

DNA; RNA;

EID: 42549117698     PISSN: 0393974X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Editorial
Times cited : (15)

References (63)
  • 1
    • 33751525325 scopus 로고    scopus 로고
    • Array-based comparative genomic hybridization and copy number variation in cancer research
    • Cho EK, Tchinda J, Freeman JL, Chung YJ, Cai WW, Lee C. Array-based comparative genomic hybridization and copy number variation in cancer research. Cytogenet Genome Res 2006; 115:262-72.
    • (2006) Cytogenet Genome Res , vol.115 , pp. 262-272
    • Cho, E.K.1    Tchinda, J.2    Freeman, J.L.3    Chung, Y.J.4    Cai, W.W.5    Lee, C.6
  • 3
    • 33751194901 scopus 로고    scopus 로고
    • Application of array-based comparative genomic hybridization to clinical diagnostics
    • Bejjani BA, Shaffer LG. Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 2006; 8(5):528-33.
    • (2006) J Mol Diagn , vol.8 , Issue.5 , pp. 528-533
    • Bejjani, B.A.1    Shaffer, L.G.2
  • 5
    • 23444459574 scopus 로고    scopus 로고
    • Array CGH technologies and their applications to cancer genomes
    • Davies JJ, Wilson IM, Lam WL. Array CGH technologies and their applications to cancer genomes. Chromosome Res 2005; 13(3):237-48.
    • (2005) Chromosome Res , vol.13 , Issue.3 , pp. 237-248
    • Davies, J.J.1    Wilson, I.M.2    Lam, W.L.3
  • 6
    • 9444222468 scopus 로고    scopus 로고
    • Microarray-based comparative genomic hybridization and its applications in human genetics
    • Oostlander AE, Meijer GA, Ylstra B. Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet 2004; 66(6):488-95.
    • (2004) Clin Genet , vol.66 , Issue.6 , pp. 488-495
    • Oostlander, A.E.1    Meijer, G.A.2    Ylstra, B.3
  • 9
    • 0036270889 scopus 로고    scopus 로고
    • ChIP-chip: A genomic approach for identifying transcription factor binding sites
    • Horak CE, Snyder M. ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 2002; 350:469-83.
    • (2002) Methods Enzymol , vol.350 , pp. 469-483
    • Horak, C.E.1    Snyder, M.2
  • 10
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004; 83:349-60.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 11
    • 33750906569 scopus 로고    scopus 로고
    • DNA microarray analysis of pulmonary fibrosis three months after exposure to paraquat in rats
    • Satomi Y, Tsuchiya W, Miura D, Kasahara Y, Akahori F. DNA microarray analysis of pulmonary fibrosis three months after exposure to paraquat in rats. J Toxicol Sci 2006; 31:345-55.
    • (2006) J Toxicol Sci , vol.31 , pp. 345-355
    • Satomi, Y.1    Tsuchiya, W.2    Miura, D.3    Kasahara, Y.4    Akahori, F.5
  • 14
    • 33846784074 scopus 로고    scopus 로고
    • Microarrays in breast cancer research and clinical practice - the future lies ahead
    • Gruvberger-Saal SK, Cunliffe HE, Carr KM, Hedenfalk IA. Microarrays in breast cancer research and clinical practice - the future lies ahead. Endocr Relat Cancer 2006; 13(4):1017-31.
    • (2006) Endocr Relat Cancer , vol.13 , Issue.4 , pp. 1017-1031
    • Gruvberger-Saal, S.K.1    Cunliffe, H.E.2    Carr, K.M.3    Hedenfalk, I.A.4
  • 15
    • 33750341417 scopus 로고    scopus 로고
    • Gene expression profiles of primary breast carcinomas from patients at high risk for local recurrence after breast-conserving therapy
    • Kreike B, Halfwerk H, Kristel P, Glas A, Peterse H, Bartelink H, van de Vijver MJ. Gene expression profiles of primary breast carcinomas from patients at high risk for local recurrence after breast-conserving therapy. Clin Cancer Res 2006; 12:5705-12.
    • (2006) Clin Cancer Res , vol.12 , pp. 5705-5712
    • Kreike, B.1    Halfwerk, H.2    Kristel, P.3    Glas, A.4    Peterse, H.5    Bartelink, H.6    van de Vijver, M.J.7
  • 17
    • 33748469397 scopus 로고    scopus 로고
    • Acute leukemia: Subtype discovery and prediction of outcome by gene expression profiling
    • Downing JR. Acute leukemia: subtype discovery and prediction of outcome by gene expression profiling, Verh Dtsch Ges Pathol 2003; 87:66-71.
    • (2003) Verh Dtsch Ges Pathol , vol.87 , pp. 66-71
    • Downing, J.R.1
  • 22
    • 34249785105 scopus 로고    scopus 로고
    • A Microarray Analysis of the Temporal Response of Liver to Methylprednisolone: A Comparative Analysis of Two Dosing Regimens
    • Almon RR, Dubois DC, Jusko WJ. A Microarray Analysis of the Temporal Response of Liver to Methylprednisolone: A Comparative Analysis of Two Dosing Regimens, Endocrinology 2007; 148: 2209-25.
    • (2007) Endocrinology , vol.148 , pp. 2209-2225
    • Almon, R.R.1    Dubois, D.C.2    Jusko, W.J.3
  • 24
    • 33845950511 scopus 로고    scopus 로고
    • Gefitinib-related gene signature in bladder cancer cells identified by a cDNA microarray
    • Inoue R, Matsuyama H, Yano S, Yamamoto Y, Iizuka N, Naito K. Gefitinib-related gene signature in bladder cancer cells identified by a cDNA microarray. Anticancer Res 2006; 26(6B):4195-202.
    • (2006) Anticancer Res , vol.26 , Issue.6 B , pp. 4195-4202
    • Inoue, R.1    Matsuyama, H.2    Yano, S.3    Yamamoto, Y.4    Iizuka, N.5    Naito, K.6
  • 25
    • 27144459430 scopus 로고    scopus 로고
    • Gene expression profile associated with response to doxorubicin-based therapy in breast cancer
    • Folgueira MA, Carraro DM, Brentani H et al. Gene expression profile associated with response to doxorubicin-based therapy in breast cancer. Clin Cancer Res 2005; 11:7434-43.
    • (2005) Clin Cancer Res , vol.11 , pp. 7434-7443
    • Folgueira, M.A.1    Carraro, D.M.2    Brentani, H.3
  • 26
    • 24344444819 scopus 로고    scopus 로고
    • Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer
    • Yang SX, Simon RM, Tan AR, Nguyen D, Swain SM. Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer. Clin Cancer Res 2005; 11: 6226-32.
    • (2005) Clin Cancer Res , vol.11 , pp. 6226-6232
    • Yang, S.X.1    Simon, R.M.2    Tan, A.R.3    Nguyen, D.4    Swain, S.M.5
  • 27
    • 33846681611 scopus 로고    scopus 로고
    • Clinical utility of microarray-derived genetic signatures in predicting outcomes in prostate cancer
    • Reddy GK, Balk SP. Clinical utility of microarray-derived genetic signatures in predicting outcomes in prostate cancer. Clin Genitourin Cancer 2006; 5(3): 187-9.
    • (2006) Clin Genitourin Cancer , vol.5 , Issue.3 , pp. 187-189
    • Reddy, G.K.1    Balk, S.P.2
  • 30
    • 33846978784 scopus 로고    scopus 로고
    • Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    • Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007; 99(2):147-57.
    • (2007) J Natl Cancer Inst , vol.99 , Issue.2 , pp. 147-157
    • Dupuy, A.1    Simon, R.M.2
  • 31
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: A multiple random validation strategy
    • Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005; 365(9458):488-92.
    • (2005) Lancet , vol.365 , Issue.9458 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 32
    • 8444225398 scopus 로고    scopus 로고
    • Interpretation of expression-profiling results obtained from different platforms and tissue sources: Examples using prostate cancer data
    • Chiorino G, Acquadro F, Mello Grand M, Viscomi S, Segir R, Gasparini M, Dotto P. Interpretation of expression-profiling results obtained from different platforms and tissue sources: examples using prostate cancer data. Eur J Cancer 2004; 40:2592-603.
    • (2004) Eur J Cancer , vol.40 , pp. 2592-2603
    • Chiorino, G.1    Acquadro, F.2    Mello Grand, M.3    Viscomi, S.4    Segir, R.5    Gasparini, M.6    Dotto, P.7
  • 34
    • 33748491718 scopus 로고    scopus 로고
    • Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
    • Patterson TA, Lobenhofer EK, Fulmer-Smentek SB et al. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 2006; 24: 1140-50.
    • (2006) Nat Biotechnol , vol.24 , pp. 1140-1150
    • Patterson, T.A.1    Lobenhofer, E.K.2    Fulmer-Smentek, S.B.3
  • 35
    • 33746108159 scopus 로고    scopus 로고
    • A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    • Kuo WP, Liu F, Trimarchi J, et al. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006; 24:832-40.
    • (2006) Nat Biotechnol , vol.24 , pp. 832-840
    • Kuo, W.P.1    Liu, F.2    Trimarchi, J.3
  • 36
    • 1542469713 scopus 로고    scopus 로고
    • Measurement of gene expression in archival paraffin-embedded tissues: Development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay
    • Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol 2004; 164:35-42.
    • (2004) Am J Pathol , vol.164 , pp. 35-42
    • Cronin, M.1    Pho, M.2    Dutta, D.3    Stephans, J.C.4    Shak, S.5    Kiefer, M.C.6    Esteban, J.M.7    Baker, J.B.8
  • 37
    • 0035134463 scopus 로고    scopus 로고
    • Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue
    • Specht K, Richter T, Muller U, Walch A, Werner M, Hofler H. Quantitative gene expression analysis in microdissected archival formalin-fixed and paraffin-embedded tumor tissue. Am J Pathol 2001; 158:419-29.
    • (2001) Am J Pathol , vol.158 , pp. 419-429
    • Specht, K.1    Richter, T.2    Muller, U.3    Walch, A.4    Werner, M.5    Hofler, H.6
  • 38
    • 33646240135 scopus 로고    scopus 로고
    • Two-dimensional transcriptome profiling: Identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens
    • Li HR, Wang-Rodriguez J, Nair TM et al. Two-dimensional transcriptome profiling: identification of messenger RNA isoform signatures in prostate cancer from archived paraffin-embedded cancer specimens. Cancer Res 2006; 66:4079-88.
    • (2006) Cancer Res , vol.66 , pp. 4079-4088
    • Li, H.R.1    Wang-Rodriguez, J.2    Nair, T.M.3
  • 39
    • 33845759906 scopus 로고    scopus 로고
    • Comparative analysis of a 3′ end tag PCR and a linear RNA amplification approach for microarray analysis
    • Laurell C, Wirta V, Nilsson P, Lundeberg J. Comparative analysis of a 3′ end tag PCR and a linear RNA amplification approach for microarray analysis. J Biotechnol 2007; 127: 638-46.
    • (2007) J Biotechnol , vol.127 , pp. 638-646
    • Laurell, C.1    Wirta, V.2    Nilsson, P.3    Lundeberg, J.4
  • 40
    • 33744549560 scopus 로고    scopus 로고
    • In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays
    • Ma C, Lyons-Weiler M, Liang W, LaFramboise W, Gilbertson JR, Becich MJ, Monzon FA. In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays. J Mol Diagn 2006; 8:183-92.
    • (2006) J Mol Diagn , vol.8 , pp. 183-192
    • Ma, C.1    Lyons-Weiler, M.2    Liang, W.3    LaFramboise, W.4    Gilbertson, J.R.5    Becich, M.J.6    Monzon, F.A.7
  • 43
    • 33846986793 scopus 로고    scopus 로고
    • Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips
    • Stalteri MA, Harrison AP. Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. BMC Bioinformatics 2007; 8:13.
    • (2007) BMC Bioinformatics , vol.8 , pp. 13
    • Stalteri, M.A.1    Harrison, A.P.2
  • 45
    • 20144386497 scopus 로고    scopus 로고
    • Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays
    • Stolc V, Samanta MP, Tongprasit W et al. Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci USA 2005; 102:4453-8.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 4453-4458
    • Stolc, V.1    Samanta, M.P.2    Tongprasit, W.3
  • 46
    • 26444502673 scopus 로고    scopus 로고
    • A microarray configuration to quantify expression levels and relative abundance of splice variants
    • Fehlbaum P, Guihal C, Bracco L, Cochet O. A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucl Acids Res 2005; 33:e47.
    • (2005) Nucl Acids Res , vol.33
    • Fehlbaum, P.1    Guihal, C.2    Bracco, L.3    Cochet, O.4
  • 47
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • Jeffery IB et al. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics. 2006; 7:359-366.
    • (2006) BMC Bioinformatics , vol.7 , pp. 359-366
    • Jeffery, I.B.1
  • 48
    • 0028220393 scopus 로고
    • Advances in statistical methodology for the evaluation of diagnostic and laboratory tests
    • Chambell G. Advances in statistical methodology for the evaluation of diagnostic and laboratory tests. Statistics in Medicine 1994; 13:499-508.
    • (1994) Statistics in Medicine , vol.13 , pp. 499-508
    • Chambell, G.1
  • 49
    • 14044252027 scopus 로고    scopus 로고
    • Multiple testing. Part I. Single-step procedures for control of general type I error rates
    • Dudoit S, van der Laan MJ, Pollard KS. "Multiple testing. Part I. Single-step procedures for control of general type I error rates." Stat Appl Genet Mol Biol 2004; 3:13-21.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 13-21
    • Dudoit, S.1    van der Laan, M.J.2    Pollard, K.S.3
  • 50
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004; 3:3-9.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 3-9
    • Smyth, G.K.1
  • 54
    • 0029355897 scopus 로고
    • Establishing a human transcript map
    • Boguski MS, Schuler GD. "Establishing a human transcript map." Nat Genet 1995; 10:369-371.
    • (1995) Nat Genet , vol.10 , pp. 369-371
    • Boguski, M.S.1    Schuler, G.D.2
  • 55
    • 0037252705 scopus 로고    scopus 로고
    • Database Resources of the National Center for Biotechnology
    • Wheeler DL et al. Database Resources of the National Center for Biotechnology. Nucl Acids Res 2003; 31:28-33.
    • (2003) Nucl Acids Res , vol.31 , pp. 28-33
    • Wheeler, D.L.1
  • 56
    • 33750713346 scopus 로고    scopus 로고
    • GeneTools - application for functional annotation and statistical hypothesis testing
    • Beisvag V et al. GeneTools - application for functional annotation and statistical hypothesis testing. BMC Bioinformatics 2006; 7:470-77.
    • (2006) BMC Bioinformatics , vol.7 , pp. 470-477
    • Beisvag, V.1
  • 57
    • 13444273448 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt)
    • Bairoch A. The Universal Protein Resource (UniProt). Nucl Acids Res 2005; 33:D154-159.
    • (2005) Nucl Acids Res , vol.33
    • Bairoch, A.1
  • 58
    • 6044271269 scopus 로고    scopus 로고
    • Juggling between evolution and stability
    • Bairoch A. Swiss-Prot: Juggling between evolution and stability. Brief Bioinform 2004; 5:39-55.
    • (2004) Brief Bioinform , vol.5 , pp. 39-55
    • Bairoch, A.1    Prot, S.2
  • 60
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005; 21:3587-95.
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 61
    • 33845884027 scopus 로고    scopus 로고
    • Integrative molecular concept modelling of prostate cancer progression
    • Tomlins SA, Mehra R, Rhodes DR et al. Integrative molecular concept modelling of prostate cancer progression. Nat Genet 2007; 39:41-51.
    • (2007) Nat Genet , vol.39 , pp. 41-51
    • Tomlins, S.A.1    Mehra, R.2    Rhodes, D.R.3


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