메뉴 건너뛰기




Volumn 15, Issue 1, 2004, Pages 52-57

Statistical analysis of global gene expression data: Some practical considerations

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; OLIGOMER;

EID: 1242351300     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2003.12.004     Document Type: Review
Times cited : (25)

References (63)
  • 1
    • 0026108692 scopus 로고
    • Light-directed, spatially addressable parallel chemical synthesis
    • Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 251:1991;767-773.
    • (1991) Science , vol.251 , pp. 767-773
    • Fodor, S.P.1    Read, J.L.2    Pirrung, M.C.3    Stryer, L.4    Lu, A.T.5    Solas, D.6
  • 2
    • 84984932880 scopus 로고    scopus 로고
    • Array of hope
    • Lander E.S. Array of hope. Nat. Genet. 21(Suppl 1):1999;3-4.
    • (1999) Nat. Genet. , vol.21 , Issue.SUPPL. 1 , pp. 3-4
    • Lander, E.S.1
  • 8
    • 1242300778 scopus 로고    scopus 로고
    • Cambridge, UK: Cambridge University Press;
    • Stekel D: Microarray Bioinformatics. Cambridge, UK: Cambridge University Press; 2003.
    • (2003) Microarray Bioinformatics
    • Stekel, D.1
  • 9
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • Reiner A., Yekutieli D., 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
  • 10
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • Li C., Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA. 98:2001;31-36.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 11
    • 0042121250 scopus 로고    scopus 로고
    • ChipInfo: Software for extracting gene annotation and gene ontology information for microarray analysis
    • ChipInfo is one of the first comprehensive model-based approaches to analyze oligo arrays.
    • Zhong S., Li C., Wong W.H. ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res. 31:2003;3483-3486 ChipInfo is one of the first comprehensive model-based approaches to analyze oligo arrays.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3483-3486
    • Zhong, S.1    Li, C.2    Wong, W.H.3
  • 12
    • 0035875553 scopus 로고    scopus 로고
    • Issues in cDNA microarray analysis: Quality filtering, channel normalization, models of variations and assessment of gene effects
    • Tseng G.C., Oh M.K., Rohlin L., Liao J.C., Wong W.H. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic Acids Res. 29:2001;2549-2557.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2549-2557
    • Tseng, G.C.1    Oh, M.K.2    Rohlin, L.3    Liao, J.C.4    Wong, W.H.5
  • 13
    • 0142042997 scopus 로고    scopus 로고
    • A software package for cDNA microarray data normalization and assessing confidence intervals
    • lcDNA generates confidence intervals for each gene in two-channel cDNA array experiments.
    • Hyduke D.R., Rohlin L., Kao K.C., Liao J.C. A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS. 7:2003;227-234 lcDNA generates confidence intervals for each gene in two-channel cDNA array experiments.
    • (2003) OMICS , vol.7 , pp. 227-234
    • Hyduke, D.R.1    Rohlin, L.2    Kao, K.C.3    Liao, J.C.4
  • 15
    • 0036713509 scopus 로고    scopus 로고
    • Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
    • Tjaden B.C., Saxoni R., Stolyar S., Haynor D., Kolker E., Rosenow C. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30:2002;3732-3738.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3732-3738
    • Tjaden, B.C.1    Saxoni, R.2    Stolyar, S.3    Haynor, D.4    Kolker, E.5    Rosenow, C.6
  • 22
    • 0036266113 scopus 로고    scopus 로고
    • Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis
    • Kivi M., Liu X., Raychaudhuri S., Altman R.B., Small P.M. Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. J. Clin. Microbiol. 40:2002;2192-2198.
    • (2002) J. Clin. Microbiol. , vol.40 , pp. 2192-2198
    • Kivi, M.1    Liu, X.2    Raychaudhuri, S.3    Altman, R.B.4    Small, P.M.5
  • 23
    • 0037461024 scopus 로고    scopus 로고
    • Automatic analysis of DNA microarray images using mathematical morphology
    • Angulo J., Serra J. Automatic analysis of DNA microarray images using mathematical morphology. Bioinformatics. 19:2003;553-562.
    • (2003) Bioinformatics , vol.19 , pp. 553-562
    • Angulo, J.1    Serra, J.2
  • 24
    • 0037314037 scopus 로고    scopus 로고
    • Combinatorial image analysis of DNA microarray features
    • Glasbey C.A., Ghazal P. Combinatorial image analysis of DNA microarray features. Bioinformatics. 19:2003;194-198.
    • (2003) Bioinformatics , vol.19 , pp. 194-198
    • Glasbey, C.A.1    Ghazal, P.2
  • 25
    • 0036855423 scopus 로고    scopus 로고
    • SNOMAD (standardization and normalization of microarray data): Web-accessible gene expression data analysis
    • Colantuoni C., Henry G., Zeger S., Pevsner J. SNOMAD (standardization and normalization of microarray data): web-accessible gene expression data analysis. Bioinformatics. 18:2002;1540-1541.
    • (2002) Bioinformatics , vol.18 , pp. 1540-1541
    • Colantuoni, C.1    Henry, G.2    Zeger, S.3    Pevsner, J.4
  • 26
    • 0037188875 scopus 로고    scopus 로고
    • Normalization and analysis of DNA microarray data by self-consistency and local regression
    • RESEARCH0037.
    • Kepler TB, Morgan KT: Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biol 2002, 3:RESEARCH0037.
    • (2002) Genome Biol , pp. 3
    • Kepler, T.B.1    Morgan, K.T.2
  • 28
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30:2002;E15-E25.
    • (2002) Nucleic Acids Res. , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 30
    • 0035999977 scopus 로고    scopus 로고
    • A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    • Pan W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics. 18:2002;546-554.
    • (2002) Bioinformatics , vol.18 , pp. 546-554
    • Pan, W.1
  • 31
    • 12244298154 scopus 로고    scopus 로고
    • Statistical analysis of high-density oligonucleotide arrays: A multiplicative noise model
    • Sasik R., Calvo E., Corbeil J. Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics. 18:2002;1633-1640.
    • (2002) Bioinformatics , vol.18 , pp. 1633-1640
    • Sasik, R.1    Calvo, E.2    Corbeil, J.3
  • 33
    • 0036211063 scopus 로고    scopus 로고
    • Analysis of matched mRNA measurements from two different microarray technologies
    • These two references discuss the difficulties in cross-platform comparisons of expression experiments.
    • Kuo W.P., Jenssen T.K., Butte A.J., Ohno-Machado L., Kohane I.S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics. 18:2002;405-412 These two references discuss the difficulties in cross-platform comparisons of expression experiments.
    • (2002) Bioinformatics , vol.18 , pp. 405-412
    • Kuo, W.P.1    Jenssen, T.K.2    Butte, A.J.3    Ohno-Machado, L.4    Kohane, I.S.5
  • 35
    • 0035024021 scopus 로고    scopus 로고
    • Validating clustering for gene expression data
    • Yeung K.Y., Haynor D.R., Ruzzo W.L. Validating clustering for gene expression data. Bioinformatics. 17:2001;309-318.
    • (2001) Bioinformatics , vol.17 , pp. 309-318
    • Yeung, K.Y.1    Haynor, D.R.2    Ruzzo, W.L.3
  • 36
    • 0037342510 scopus 로고    scopus 로고
    • Comparisons and validation of statistical clustering techniques for microarray gene expression data
    • Datta S. Comparisons and validation of statistical clustering techniques for microarray gene expression data. Bioinformatics. 19:2003;459-466.
    • (2003) Bioinformatics , vol.19 , pp. 459-466
    • Datta, S.1
  • 37
    • 0043194165 scopus 로고    scopus 로고
    • Shrinkage-based similarity metric for cluster analysis of microarray data
    • Cherepinsky V., Feng J., Rejali M., Mishra B. Shrinkage-based similarity metric for cluster analysis of microarray data. Proc. Natl. Acad. Sci. USA. 100:2003;9668-9673.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9668-9673
    • Cherepinsky, V.1    Feng, J.2    Rejali, M.3    Mishra, B.4
  • 38
    • 0036677672 scopus 로고    scopus 로고
    • Mapping physiological states from microarray expression measurements
    • Stephanopoulos G., Hwang D., Schmitt W.A., Misra J. Mapping physiological states from microarray expression measurements. Bioinformatics. 18:2002;1054-1063.
    • (2002) Bioinformatics , vol.18 , pp. 1054-1063
    • Stephanopoulos, G.1    Hwang, D.2    Schmitt, W.A.3    Misra, J.4
  • 39
    • 0035367064 scopus 로고    scopus 로고
    • Whole-genome expression analysis: Challenges beyond clustering
    • Altman R.B., Raychaudhuri S. Whole-genome expression analysis: challenges beyond clustering. Curr. Opin. Struct. Biol. 11:2001;340-347.
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 340-347
    • Altman, R.B.1    Raychaudhuri, S.2
  • 40
    • 0036489046 scopus 로고    scopus 로고
    • Comparison of discriminative methods for the classification of tumors using gene expression data
    • Dudoit S., Fridlyand J., Speed T.P. Comparison of discriminative methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc. 97:2002;77-87.
    • (2002) J. Am. Stat. Assoc. , vol.97 , pp. 77-87
    • Dudoit, S.1    Fridlyand, J.2    Speed, T.P.3
  • 41
    • 0036855903 scopus 로고    scopus 로고
    • Statistical analysis of a small set of time-ordered gene expression data using linear splines
    • De Hoon M.J., Imoto S., Miyano S. Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics. 18:2002;1477-1485.
    • (2002) Bioinformatics , vol.18 , pp. 1477-1485
    • De Hoon, M.J.1    Imoto, S.2    Miyano, S.3
  • 43
    • 0037270514 scopus 로고    scopus 로고
    • Towards reconstruction of gene networks from expression data by supervised learning
    • Soinov L.A., Krestyaninova M.A., Brazma A. Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol. 4:2003;R6.
    • (2003) Genome Biol. , vol.4 , pp. 6
    • Soinov, L.A.1    Krestyaninova, M.A.2    Brazma, A.3
  • 44
    • 0037335024 scopus 로고    scopus 로고
    • Experimental design of DNA microarray experiments
    • Simon R., Dobbin K. Experimental design of DNA microarray experiments. Biotechniques. 34(Suppl 1):2003;16-21.
    • (2003) Biotechniques , vol.34 , Issue.SUPPL. 1 , pp. 16-21
    • Simon, R.1    Dobbin, K.2
  • 45
    • 0034730124 scopus 로고    scopus 로고
    • Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
    • Lee M.L., Kuo F.C., Whitmore G.A., Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA. 97:2000;9834-9839.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 9834-9839
    • Lee, M.L.1    Kuo, F.C.2    Whitmore, G.A.3    Sklar, J.4
  • 46
    • 0000884487 scopus 로고    scopus 로고
    • Experimental design for gene expression microarrays
    • Important study of experimental designs for gene expression experiments.
    • Kerr M.K., Churchill G.A. Experimental design for gene expression microarrays. Biostatistics. 2:2001;183-201 Important study of experimental designs for gene expression experiments.
    • (2001) Biostatistics , vol.2 , pp. 183-201
    • Kerr, M.K.1    Churchill, G.A.2
  • 48
    • 0242606431 scopus 로고    scopus 로고
    • Microrarrays: How many do you need?
    • Easy-to-use internet service aimed at estimating the number of arrays to be used per experiment.
    • Zien A., Fluck J., Zimmer R., Lengauer T. Microrarrays: how many do you need? J. Comput. Biol. 10:2003;653-667 Easy-to-use internet service aimed at estimating the number of arrays to be used per experiment.
    • (2003) J. Comput. Biol. , vol.10 , pp. 653-667
    • Zien, A.1    Fluck, J.2    Zimmer, R.3    Lengauer, T.4
  • 49
    • 0034098727 scopus 로고    scopus 로고
    • Systematic management and analysis of yeast gene expression data
    • Aach J., Rindone W., Church G.M. Systematic management and analysis of yeast gene expression data. Genome Res. 10:2000;431-445.
    • (2000) Genome Res. , vol.10 , pp. 431-445
    • Aach, J.1    Rindone, W.2    Church, G.M.3
  • 51
    • 0037174983 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K-12
    • Hung S.P., Baldi P., Hatfield G.W. Global gene expression profiling in Escherichia coli K-12. J. Biol. Chem. 277:2002;40309-40323.
    • (2002) J. Biol. Chem. , vol.277 , pp. 40309-40323
    • Hung, S.P.1    Baldi, P.2    Hatfield, G.W.3
  • 52
    • 0142244176 scopus 로고    scopus 로고
    • Post-normalization quality assessment visualization of microarray data
    • McClure J., Wit E. Post-normalization quality assessment visualization of microarray data. Comp. Funct. Genomics. 4:2003;460-467.
    • (2003) Comp. Funct. Genomics , vol.4 , pp. 460-467
    • McClure, J.1    Wit, E.2
  • 53
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest-path analysis of gene expression data
    • Zhou X., Kao M.C., Wong W.H. Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl. Acad. Sci. USA. 99:2002;12783-12788.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12783-12788
    • Zhou, X.1    Kao, M.C.2    Wong, W.H.3
  • 56
    • 0038199116 scopus 로고    scopus 로고
    • Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis
    • Tjaden B.C., Haynor D., Stolyar S., Rosenow C., Kolker E. Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. Bioinformatics. 18:2002;S337-S344.
    • (2002) Bioinformatics , vol.18
    • Tjaden, B.C.1    Haynor, D.2    Stolyar, S.3    Rosenow, C.4    Kolker, E.5
  • 57
    • 12244259677 scopus 로고    scopus 로고
    • Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
    • Qin Z.S., McCue L.A., Thompson W., Mayerhofer L., Lawrence C.E., Liu J.S. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. Nat. Biotechnol. 21:2003;435-439.
    • (2003) Nat. Biotechnol. , vol.21 , pp. 435-439
    • Qin, Z.S.1    McCue, L.A.2    Thompson, W.3    Mayerhofer, L.4    Lawrence, C.E.5    Liu, J.S.6
  • 61
    • 0041923788 scopus 로고    scopus 로고
    • Toward a protein profile of Escherichia coli: Comparison to its transcription profile
    • These four studies complement expression experiments with other types of information.
    • Corbin R.W., Paliy O., Yang F., Shabanowitz J., Platt M., Lyons C.E. Jr., Root K., McAuliffe J., Jordan M.I., Kustu S.et al. Toward a protein profile of Escherichia coli: comparison to its transcription profile. Proc. Natl. Acad. Sci. USA. 100:2003;9232-9237 These four studies complement expression experiments with other types of information.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9232-9237
    • Corbin, R.W.1    Paliy, O.2    Yang, F.3    Shabanowitz, J.4    Platt, M.5    Lyons, C.E.Jr.6    Root, K.7    McAuliffe, J.8    Jordan, M.I.9    Kustu, S.10
  • 63
    • 84883549310 scopus 로고    scopus 로고
    • Microarray data analysis Database. URL: http://www.nslij-genetics.org/ microarray/ These websites represent wide-ranging compilations of literature, methods and analysis tools for microarrays.
    • Microarray Data Analysis Database


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.