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Volumn 14, Issue , 2008, Pages 29-61

Gene expression microarray data analysis demystified

Author keywords

clustering; correction for multiple testing; cross platform comparison; gene expression; gene ontology; microarray; microarray data analysis; normalization; pathway; preprocessing; statistical analysis

Indexed keywords

CLINICAL DATA REPOSITORY; CONTROLLED STUDY; DATA ANALYSIS; EXPERIMENTAL DESIGN; GENE EXPRESSION; GENE TECHNOLOGY; MICROARRAY ANALYSIS; REVIEW; STATISTICAL ANALYSIS;

EID: 46149122759     PISSN: 13872656     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1387-2656(08)00002-1     Document Type: Review
Times cited : (22)

References (125)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 46149101388 scopus 로고    scopus 로고
    • R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2007.
    • R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2007.
  • 5
    • 29244448340 scopus 로고    scopus 로고
    • Microarray data analysis: from disarray to consolidation and consensus
    • Allison D.B., Cui X., Page G.P., and Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7 (2006) 55-65
    • (2006) Nat Rev Genet , vol.7 , pp. 55-65
    • Allison, D.B.1    Cui, X.2    Page, G.P.3    Sabripour, M.4
  • 6
    • 33745407776 scopus 로고    scopus 로고
    • The microarray data analysis process: from raw data to biological significance
    • Olson N.E. The microarray data analysis process: from raw data to biological significance. NeuroRx 3 (2006) 373-383
    • (2006) NeuroRx , vol.3 , pp. 373-383
    • Olson, N.E.1
  • 7
    • 34347334547 scopus 로고    scopus 로고
    • What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments
    • Kerr K.F., Serikawa K.A., Wei C., Peters M.A., and Bumgarner R.E. What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments. OMICS 11 (2007) 152-165
    • (2007) OMICS , vol.11 , pp. 152-165
    • Kerr, K.F.1    Serikawa, K.A.2    Wei, C.3    Peters, M.A.4    Bumgarner, R.E.5
  • 11
    • 3042855581 scopus 로고    scopus 로고
    • Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression
    • Chou C., Chen C., Lee T., and Peck K. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res 32 (2004) e99
    • (2004) Nucleic Acids Res , vol.32
    • Chou, C.1    Chen, C.2    Lee, T.3    Peck, K.4
  • 12
    • 9144256854 scopus 로고    scopus 로고
    • Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations
    • Shippy R., Sendera T.J., Lockner R., Palaniappan C., Kaysser-Kranich T., Watts G., and Alsobrook J. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5 (2004) 61
    • (2004) BMC Genomics , vol.5 , pp. 61
    • Shippy, R.1    Sendera, T.J.2    Lockner, R.3    Palaniappan, C.4    Kaysser-Kranich, T.5    Watts, G.6    Alsobrook, J.7
  • 14
    • 0037458085 scopus 로고    scopus 로고
    • Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression
    • Barrett J.C., and Kawasaki E.S. Microarrays: the use of oligonucleotides and cDNA for the analysis of gene expression. Drug Discov Today 8 (2003) 134-141
    • (2003) Drug Discov Today , vol.8 , pp. 134-141
    • Barrett, J.C.1    Kawasaki, E.S.2
  • 15
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt K.D., Tatusova T., and Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35 (2007) D61-D65
    • (2007) Nucleic Acids Res , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 18
    • 0031256078 scopus 로고    scopus 로고
    • Pieces of the puzzle: expressed sequence tags and the catalog of human genes
    • Schuler G.D. Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J Mol Med 75 (1997) 1432-1440
    • (1997) J Mol Med , vol.75 , pp. 1432-1440
    • Schuler, G.D.1
  • 20
    • 26444454986 scopus 로고    scopus 로고
    • A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array
    • Harbig J., Sprinkle R., and Enkemann S.A. A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 33 (2005) e31
    • (2005) Nucleic Acids Res , vol.33
    • Harbig, J.1    Sprinkle, R.2    Enkemann, S.A.3
  • 21
    • 25444515422 scopus 로고    scopus 로고
    • Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    • Carter S.L., Eklund A.C., Mecham B.H., Kohane I.S., and Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 6 (2005) 107
    • (2005) BMC Bioinformatics , vol.6 , pp. 107
    • Carter, S.L.1    Eklund, A.C.2    Mecham, B.H.3    Kohane, I.S.4    Szallasi, Z.5
  • 23
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • Draghici S., Khatri P., Eklund A.C., and Szallasi Z. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22 (2006) 101-109
    • (2006) Trends Genet , vol.22 , pp. 101-109
    • Draghici, S.1    Khatri, P.2    Eklund, A.C.3    Szallasi, Z.4
  • 24
    • 33746361200 scopus 로고    scopus 로고
    • Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations
    • Okoniewski M.J., and Miller C.J. Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics 7 (2006) 276
    • (2006) BMC Bioinformatics , vol.7 , pp. 276
    • Okoniewski, M.J.1    Miller, C.J.2
  • 25
    • 34249699749 scopus 로고    scopus 로고
    • A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat
    • Alberts R., Terpstra P., Hardonk M., Bystrykh L.V., de Haan G., Breitling R., Nap J., and Jansen R.C. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat. BMC Bioinformatics 8 (2007) 132
    • (2007) BMC Bioinformatics , vol.8 , pp. 132
    • Alberts, R.1    Terpstra, P.2    Hardonk, M.3    Bystrykh, L.V.4    de Haan, G.5    Breitling, R.6    Nap, J.7    Jansen, R.C.8
  • 26
    • 0346733313 scopus 로고    scopus 로고
    • Design considerations for efficient and effective microarray studies
    • Kerr M.K. Design considerations for efficient and effective microarray studies. Biometrics 59 (2003) 822-828
    • (2003) Biometrics , vol.59 , pp. 822-828
    • Kerr, M.K.1
  • 28
    • 0036319960 scopus 로고    scopus 로고
    • Design issues for cDNA microarray experiments
    • Yang Y.H., and Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet 3 (2002) 579-588
    • (2002) Nat Rev Genet , vol.3 , pp. 579-588
    • Yang, Y.H.1    Speed, T.2
  • 29
    • 8844224836 scopus 로고    scopus 로고
    • A statistical framework for the design of microarray experiments and effective detection of differential gene expression
    • Zhang S., and Gant T.W. A statistical framework for the design of microarray experiments and effective detection of differential gene expression. Bioinformatics 20 (2004) 2821-2828
    • (2004) Bioinformatics , vol.20 , pp. 2821-2828
    • Zhang, S.1    Gant, T.W.2
  • 31
    • 0036051492 scopus 로고    scopus 로고
    • How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach
    • research0022
    • Pan W., Lin J., and Le C.T. How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach. Genome Biol 3 (2002) research0022
    • (2002) Genome Biol , vol.3
    • Pan, W.1    Lin, J.2    Le, C.T.3
  • 32
    • 0141626917 scopus 로고    scopus 로고
    • The effect of replication on gene expression microarray experiments
    • Pavlidis P., Li Q., and Noble W.S. The effect of replication on gene expression microarray experiments. Bioinformatics 19 (2003) 1620-1627
    • (2003) Bioinformatics , vol.19 , pp. 1620-1627
    • Pavlidis, P.1    Li, Q.2    Noble, W.S.3
  • 33
    • 1842680967 scopus 로고    scopus 로고
    • Reproducibility, sources of variability, pooling, and sample size: important considerations for the design of high-density oligonucleotide array experiments
    • Han E., Wu Y., McCarter R., Nelson J.F., Richardson A., and Hilsenbeck S.G. Reproducibility, sources of variability, pooling, and sample size: important considerations for the design of high-density oligonucleotide array experiments. J Gerontol A Biol Sci Med Sci 59 (2004) 306-315
    • (2004) J Gerontol A Biol Sci Med Sci , vol.59 , pp. 306-315
    • Han, E.1    Wu, Y.2    McCarter, R.3    Nelson, J.F.4    Richardson, A.5    Hilsenbeck, S.G.6
  • 34
    • 9444266425 scopus 로고    scopus 로고
    • Sample size for detecting differentially expressed genes in microarray experiments
    • Wei C., Li J., and Bumgarner R.E. Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics 5 (2004) 87
    • (2004) BMC Genomics , vol.5 , pp. 87
    • Wei, C.1    Li, J.2    Bumgarner, R.E.3
  • 35
    • 17444387485 scopus 로고    scopus 로고
    • Sample size for gene expression microarray experiments
    • Tsai C., Wang S., Chen D., and Chen J.J. Sample size for gene expression microarray experiments. Bioinformatics 21 (2005) 1502-1508
    • (2005) Bioinformatics , vol.21 , pp. 1502-1508
    • Tsai, C.1    Wang, S.2    Chen, D.3    Chen, J.J.4
  • 36
    • 17244381413 scopus 로고    scopus 로고
    • There is no silver bullet - a guide to low-level data transforms and normalisation methods for microarray data
    • Kreil D.P., and Russell R.R. There is no silver bullet - a guide to low-level data transforms and normalisation methods for microarray data. Brief Bioinform 6 (2005) 86-97
    • (2005) Brief Bioinform , vol.6 , pp. 86-97
    • Kreil, D.P.1    Russell, R.R.2
  • 42
    • 37848998510 scopus 로고    scopus 로고
    • Extended analysis of benchmark datasets for Agilent two-color microarrays
    • Kerr K.F. Extended analysis of benchmark datasets for Agilent two-color microarrays. BMC Bioinformatics 8 (2007) 371
    • (2007) BMC Bioinformatics , vol.8 , pp. 371
    • Kerr, K.F.1
  • 43
    • 33644850222 scopus 로고    scopus 로고
    • Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling
    • Nygaard V., and Hovig E. Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res 34 (2006) 996-1014
    • (2006) Nucleic Acids Res , vol.34 , pp. 996-1014
    • Nygaard, V.1    Hovig, E.2
  • 44
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad B.M., Irizarry R.A., Astrand M., and Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19 (2003) 185-193
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 45
    • 33645326509 scopus 로고    scopus 로고
    • Comparison of Affymetrix GeneChip expression measures
    • Irizarry R.A., Wu Z., and Jaffee H.A. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 22 (2006) 789-794
    • (2006) Bioinformatics , vol.22 , pp. 789-794
    • Irizarry, R.A.1    Wu, Z.2    Jaffee, H.A.3
  • 46
    • 33748809521 scopus 로고    scopus 로고
    • Probe set algorithms: is there a rational best bet?
    • Seo J., and Hoffman E.P. Probe set algorithms: is there a rational best bet?. BMC Bioinformatics 7 (2006) 395
    • (2006) BMC Bioinformatics , vol.7 , pp. 395
    • Seo, J.1    Hoffman, E.P.2
  • 47
    • 46149094326 scopus 로고    scopus 로고
    • Affymetrix. New statistical algorithms for monitoring gene expression on GeneChip probe arrays Technical Note. 2001.
    • Affymetrix. New statistical algorithms for monitoring gene expression on GeneChip probe arrays Technical Note. 2001.
  • 50
    • 46149085332 scopus 로고    scopus 로고
    • Affymetrix. Guide to probe logarithmic intensity error (PLIER) estimation Technical Note. 2005.
    • Affymetrix. Guide to probe logarithmic intensity error (PLIER) estimation Technical Note. 2005.
  • 55
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth G.K., and Speed T. Normalization of cDNA microarray data. Methods 31 (2003) 265-273
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 56
    • 39149111937 scopus 로고    scopus 로고
    • Lin SM, Du P and Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray. Nucleic Acids Res 2008;36:e11.
    • Lin SM, Du P and Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray. Nucleic Acids Res 2008;36:e11.
  • 58
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui X., and Churchill G.A. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4 (2003) 210
    • (2003) Genome Biol , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.A.2
  • 59
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis of microarray expression data: regularized t test and statistical inferences of gene changes
    • Baldi P., and Long A.D. A Bayesian framework for the analysis of microarray expression data: regularized t test and statistical inferences of gene changes. Bioinformatics 17 (2001) 509-519
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.D.2
  • 61
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher V.G., Tibshirani R., and Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98 (2001) 5116-5121
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 62
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • Jeffery I.B., Higgins D.G., and Culhane A.C. Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. BMC Bioinformatics 7 (2006) 359
    • (2006) BMC Bioinformatics , vol.7 , pp. 359
    • Jeffery, I.B.1    Higgins, D.G.2    Culhane, A.C.3
  • 63
    • 13244259309 scopus 로고    scopus 로고
    • Analysis of oligonucleotide array experiments with repeated measures using mixed models
    • Li H., Wood C.L., Getchell T.V., Getchell M.L., and Stromberg A.J. Analysis of oligonucleotide array experiments with repeated measures using mixed models. BMC Bioinformatics 5 (2004) 209
    • (2004) BMC Bioinformatics , vol.5 , pp. 209
    • Li, H.1    Wood, C.L.2    Getchell, T.V.3    Getchell, M.L.4    Stromberg, A.J.5
  • 64
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc. Ser B (Methodological) 57 (1995) 289-300
    • (1995) J R Stat Soc. Ser B (Methodological) , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 65
    • 0002294347 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat 6 (1979) 65-70
    • (1979) Scand J Stat , vol.6 , pp. 65-70
    • Holm, S.1
  • 67
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • Reiner A., Yekutieli D., and Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19 (2003) 368-375
    • (2003) Bioinformatics , vol.19 , pp. 368-375
    • Reiner, A.1    Yekutieli, D.2    Benjamini, Y.3
  • 69
    • 34250173397 scopus 로고    scopus 로고
    • Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures
    • Lu X., and Perkins D.L. Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures. BMC Bioinformatics 8 (2007) 157
    • (2007) BMC Bioinformatics , vol.8 , pp. 157
    • Lu, X.1    Perkins, D.L.2
  • 70
    • 33644858587 scopus 로고    scopus 로고
    • Multidimensional local false discovery rate for microarray studies
    • Ploner A., Calza S., Gusnanto A., and Pawitan Y. Multidimensional local false discovery rate for microarray studies. Bioinformatics 22 (2006) 556-565
    • (2006) Bioinformatics , vol.22 , pp. 556-565
    • Ploner, A.1    Calza, S.2    Gusnanto, A.3    Pawitan, Y.4
  • 71
    • 33847120762 scopus 로고    scopus 로고
    • Detecting differential expression in microarray data: comparison of optimal procedures
    • Perelman E., Ploner A., Calza S., and Pawitan Y. Detecting differential expression in microarray data: comparison of optimal procedures. BMC Bioinformatics 8 (2007) 28
    • (2007) BMC Bioinformatics , vol.8 , pp. 28
    • Perelman, E.1    Ploner, A.2    Calza, S.3    Pawitan, Y.4
  • 72
    • 23844434593 scopus 로고    scopus 로고
    • Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data
    • Boutros P.C., and Okey A.B. Unsupervised pattern recognition: an introduction to the whys and wherefores of clustering microarray data. Brief Bioinform 6 (2005) 331-343
    • (2005) Brief Bioinform , vol.6 , pp. 331-343
    • Boutros, P.C.1    Okey, A.B.2
  • 75
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation
    • Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., Lander E.S., and Golub T.R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96 (1999) 2907-2912
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 78
    • 33947363787 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for gene expression data
    • Datta S., and Datta S. Evaluation of clustering algorithms for gene expression data. BMC Bioinformatics 7 Suppl. 4 (2006) S17
    • (2006) BMC Bioinformatics , vol.7 , Issue.SUPPL. 4
    • Datta, S.1    Datta, S.2
  • 79
    • 0023453329 scopus 로고
    • Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
    • Rousseeuw P. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 20 (1987) 53-65
    • (1987) J Comput Appl Math , vol.20 , pp. 53-65
    • Rousseeuw, P.1
  • 81
    • 0037172724 scopus 로고    scopus 로고
    • A prediction-based resampling method for estimating the number of clusters in a dataset
    • RESEARCH0036
    • Dudoit S., and Fridlyand J. A prediction-based resampling method for estimating the number of clusters in a dataset. Genome Biol 3 (2002) RESEARCH0036
    • (2002) Genome Biol , vol.3
    • Dudoit, S.1    Fridlyand, J.2
  • 82
    • 25144456056 scopus 로고    scopus 로고
    • Computational cluster validation in post-genomic data analysis
    • Handl J., Knowles J., and Kell D.B. Computational cluster validation in post-genomic data analysis. Bioinformatics 21 (2005) 3201-3212
    • (2005) Bioinformatics , vol.21 , pp. 3201-3212
    • Handl, J.1    Knowles, J.2    Kell, D.B.3
  • 83
    • 17944394324 scopus 로고    scopus 로고
    • Fuzzy C-means method for clustering microarray data
    • Dembélé D., and Kastner P. Fuzzy C-means method for clustering microarray data. Bioinformatics 19 (2003) 973-980
    • (2003) Bioinformatics , vol.19 , pp. 973-980
    • Dembélé, D.1    Kastner, P.2
  • 84
    • 0033657261 scopus 로고    scopus 로고
    • Principal components analysis to summarize microarray experiments: application to sporulation time series
    • Raychaudhuri S., Stuart J.M., and Altman R.B. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 5 (2000) 455-466
    • (2000) Pac Symp Biocomput , vol.5 , pp. 455-466
    • Raychaudhuri, S.1    Stuart, J.M.2    Altman, R.B.3
  • 85
    • 0036166753 scopus 로고    scopus 로고
    • Linear modes of gene expression determined by independent component analysis
    • Liebermeister W. Linear modes of gene expression determined by independent component analysis. Bioinformatics 18 (2002) 51-60
    • (2002) Bioinformatics , vol.18 , pp. 51-60
    • Liebermeister, W.1
  • 86
    • 34548444625 scopus 로고    scopus 로고
    • Elucidating the altered transcriptional programs in breast cancer using independent component analysis
    • Teschendorff A.E., Journée M., Absil P.A., Sepulchre R., and Caldas C. Elucidating the altered transcriptional programs in breast cancer using independent component analysis. PLoS Comput Biol 3 (2007) e161
    • (2007) PLoS Comput Biol , vol.3
    • Teschendorff, A.E.1    Journée, M.2    Absil, P.A.3    Sepulchre, R.4    Caldas, C.5
  • 88
    • 36349010718 scopus 로고    scopus 로고
    • Gene selection for classification of microarray data based on the Bayes error
    • Zhang J., and Deng H. Gene selection for classification of microarray data based on the Bayes error. BMC Bioinformatics 8 (2007) 370
    • (2007) BMC Bioinformatics , vol.8 , pp. 370
    • Zhang, J.1    Deng, H.2
  • 89
    • 17244372135 scopus 로고    scopus 로고
    • Putting microarrays in a context: integrated analysis of diverse biological data
    • Troyanskaya O.G. Putting microarrays in a context: integrated analysis of diverse biological data. Brief Bioinform 6 (2005) 34-43
    • (2005) Brief Bioinform , vol.6 , pp. 34-43
    • Troyanskaya, O.G.1
  • 90
    • 33745699558 scopus 로고    scopus 로고
    • Current bioinformatics tools in genomic biomedical research (Review)
    • Teufel A., Krupp M., Weinmann A., and Galle P.R. Current bioinformatics tools in genomic biomedical research (Review). Int J Mol Med 17 (2006) 967-973
    • (2006) Int J Mol Med , vol.17 , pp. 967-973
    • Teufel, A.1    Krupp, M.2    Weinmann, A.3    Galle, P.R.4
  • 91
    • 34249752597 scopus 로고    scopus 로고
    • Extracting biology from high-dimensional biological data
    • Quackenbush J. Extracting biology from high-dimensional biological data. J Exp Biol 210 (2007) 1507-1517
    • (2007) J Exp Biol , vol.210 , pp. 1507-1517
    • Quackenbush, J.1
  • 93
    • 46149086707 scopus 로고    scopus 로고
    • European Biotechnology Institute: http://www.ebi.ac.uk/.
    • European Biotechnology Institute: http://www.ebi.ac.uk/.
  • 96
    • 84984996500 scopus 로고    scopus 로고
    • Gene Ontology Consortium. The Gene Ontology Project in 2008. Nucleic Acids Res 2008;36:D440-D444.
    • Gene Ontology Consortium. The Gene Ontology Project in 2008. Nucleic Acids Res 2008;36:D440-D444.
  • 97
    • 36549002108 scopus 로고    scopus 로고
    • Gene annotation and pathway mapping in KEGG
    • Aoki-Kinoshita K.F., and Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol 396 (2007) 71-92
    • (2007) Methods Mol Biol , vol.396 , pp. 71-92
    • Aoki-Kinoshita, K.F.1    Kanehisa, M.2
  • 98
    • 33846067524 scopus 로고    scopus 로고
    • PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
    • Mi H., Guo N., Kejariwal A., and Thomas P.D. PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res 35 (2007) D247-D252
    • (2007) Nucleic Acids Res , vol.35
    • Mi, H.1    Guo, N.2    Kejariwal, A.3    Thomas, P.D.4
  • 99
    • 0037263812 scopus 로고    scopus 로고
    • MAPPFinder: using gene ontology and GenMAPP to create a global gene-expression profile from microarray data
    • Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using gene ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4 (2003) R7
    • (2003) Genome Biol , vol.4
    • Doniger, S.W.1    Salomonis, N.2    Dahlquist, K.D.3    Vranizan, K.4    Lawlor, S.C.5    Conklin, B.R.6
  • 101
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: current tools, limitations, and open problems
    • Khatri P., and Drǎghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21 (2005) 3587-3595
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Drǎghici, S.2
  • 104
    • 34547555664 scopus 로고    scopus 로고
    • Conducting research on the web: 2007 update for the bioinformatics links directory
    • Fox J.A., McMillan S., and Ouellette B.F.F. Conducting research on the web: 2007 update for the bioinformatics links directory. Nucleic Acids Res 35 (2007) W3-W5
    • (2007) Nucleic Acids Res , vol.35
    • Fox, J.A.1    McMillan, S.2    Ouellette, B.F.F.3
  • 105
    • 46149085808 scopus 로고    scopus 로고
    • Microarray Gene Expression Database Society: http://www.mged.org/.
    • Microarray Gene Expression Database Society: http://www.mged.org/.
  • 110
    • 23844483247 scopus 로고    scopus 로고
    • A study of inter-lab and inter-platform agreement of DNA microarray data
    • Wang H., He X., Band M., Wilson C., and Liu L. A study of inter-lab and inter-platform agreement of DNA microarray data. BMC Genomics 6 (2005) 71
    • (2005) BMC Genomics , vol.6 , pp. 71
    • Wang, H.1    He, X.2    Band, M.3    Wilson, C.4    Liu, L.5
  • 117
    • 38349088960 scopus 로고    scopus 로고
    • Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
    • Chen J., Hsueh H., Delongchamp R., Lin C., and Tsai C. Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data. BMC Bioinformatics 8 (2007) 412
    • (2007) BMC Bioinformatics , vol.8 , pp. 412
    • Chen, J.1    Hsueh, H.2    Delongchamp, R.3    Lin, C.4    Tsai, C.5
  • 120
    • 41149106140 scopus 로고    scopus 로고
    • Common human cancer genes discovered by integrated gene-expression analysis
    • Lu Y., Yi Y., Liu P., Wen W., James M., Wang D., and You M. Common human cancer genes discovered by integrated gene-expression analysis. PLoS ONE 2 (2007) e1149
    • (2007) PLoS ONE , vol.2
    • Lu, Y.1    Yi, Y.2    Liu, P.3    Wen, W.4    James, M.5    Wang, D.6    You, M.7
  • 121
    • 36448972673 scopus 로고    scopus 로고
    • Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes
    • English S.B., and Butte A.J. Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes. Bioinformatics 23 (2007) 2910-2917
    • (2007) Bioinformatics , vol.23 , pp. 2910-2917
    • English, S.B.1    Butte, A.J.2
  • 122
    • 37648999313 scopus 로고    scopus 로고
    • Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K and Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007;104:19428-19433.
    • Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K and Lander ES. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007;104:19428-19433.
  • 124
    • 34547759761 scopus 로고    scopus 로고
    • Gene expression analysis goes digital
    • Velculescu V.E., and Kinzler K.W. Gene expression analysis goes digital. Nat Biotechnol 25 (2007) 878-880
    • (2007) Nat Biotechnol , vol.25 , pp. 878-880
    • Velculescu, V.E.1    Kinzler, K.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.