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Volumn 972, Issue , 2013, Pages 155-176

Impact of experimental noise and annotation imprecision on data quality in microarray experiments

Author keywords

Annotation; Data quality; Experimental design; Quality parameters; Standardization

Indexed keywords

RNA;

EID: 84880156267     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-337-4_10     Document Type: Article
Times cited : (3)

References (70)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary dna microarray
    • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with dna microarrays
    • Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet 21:33-37
    • (1999) Nat Genet , vol.21 , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 4
    • 44849117559 scopus 로고    scopus 로고
    • Making a new technology work: The standardization and regulation of microarrays
    • Rogers S, Cambrosio A (2007) Making a new technology work: the standardization and regulation of microarrays. Yale J Biol Med 80:165-178
    • (2007) Yale J Biol Med , vol.80 , pp. 165-178
    • Rogers, S.1    Cambrosio, A.2
  • 5
    • 1542290446 scopus 로고    scopus 로고
    • Expression pro filing-best practices for data generation and interpretation in clinical trials
    • The Tumor Analysis Best Practices Working Group
    • The Tumor Analysis Best practices Working Group (2004) Expression pro filing-best practices for data generation and interpretation in clinical trials. Nat Rev 5:229-237
    • (2004) Nat Rev , vol.5 , pp. 229-237
  • 6
    • 85083615193 scopus 로고    scopus 로고
    • http://www.fda.gov/downloads/Drugs/Guidance ComplianceRegulator yInformation/Guidances/UCM079855.pdf
  • 8
    • 33644871376 scopus 로고    scopus 로고
    • Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: Practical considerations and perspectives
    • Clarke JD, Zhu T (2006) Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives. Plant J 45:630-650
    • (2006) Plant J , vol.45 , pp. 630-650
    • Clarke, J.D.1    Zhu, T.2
  • 10
    • 84892860272 scopus 로고    scopus 로고
    • Experimental design
    • In: Scherer A (ed) Wiley, West Sussex, ISBN:978-0-470-74138-74142
    • Grass P (2009) Experimental design, pp 19-31. In: Scherer A (ed) Batch effects and noise in microarray experiments. Wiley, West Sussex, ISBN:978-0-470-74138-2
    • (2009) Batch Effects and Noise in Microarray Experiments. , pp. 19-31
    • Grass, P.1
  • 11
    • 33344473340 scopus 로고    scopus 로고
    • Bias in research studies
    • Sica GT (2006) Bias in research studies. Radiology 238:780-789
    • (2006) Radiology , vol.238 , pp. 780-789
    • Sica, G.T.1
  • 14
    • 0036369642 scopus 로고    scopus 로고
    • Dna microarrays: Their use and misuse
    • Li X, Gu WMS, Balink D (2002) DNA microarrays: their use and misuse. Microcirculation 9:13-22
    • (2002) Microcirculation , vol.9 , pp. 13-22
    • Li, X.1    Gu, W.M.S.2    Balink, D.3
  • 19
    • 13444304216 scopus 로고    scopus 로고
    • Microarrays and molecular research: Noise discovery?
    • Ioannidis JP (2005) Microarrays and molecular research: noise discovery? Lancet 365:454-455
    • (2005) Lancet , vol.365 , pp. 454-455
    • Ioannidis, J.P.1
  • 20
    • 18944394950 scopus 로고    scopus 로고
    • An array of problems
    • Frantz S (2005) An array of problems. Nat Rev Drug Discov 4:362-363
    • (2005) Nat Rev Drug Discov , vol.4 , pp. 362-363
    • Frantz, S.1
  • 21
    • 33750827097 scopus 로고    scopus 로고
    • Arrays of hope
    • Strauss E (2006) Arrays of hope. Cell 127:657-659
    • (2006) Cell , vol.127 , pp. 657-659
    • Strauss, E.1
  • 22
    • 68449102706 scopus 로고    scopus 로고
    • In praise of arrays
    • Ying L, Sarwal M (2008) In praise of arrays. Pediatr Nephrol 24:1643-1659
    • (2008) Pediatr Nephrol , vol.24 , pp. 1643-1659
    • Ying, L.1    Sarwal, M.2
  • 23
    • 7444234286 scopus 로고    scopus 로고
    • Getting the noise out of gene arrays
    • Marshall E (2004) Getting the noise out of gene arrays. Science 306:630-631
    • (2004) Science , vol.306 , pp. 630-631
    • Marshall, E.1
  • 24
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: A multiple random validation strategy
    • Michiels S, Koscielny S, Hill C (2005) Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 365:488-492
    • (2005) Lancet , vol.365 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 25
    • 33645825183 scopus 로고    scopus 로고
    • Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer
    • Ein-Dor L, Zuk O, Domany E (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103:5923-5928
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5923-5928
    • Ein-Dor, L.1    Zuk, O.2    Domany, E.3
  • 30
    • 0036356994 scopus 로고    scopus 로고
    • Assessment of the relationship between signal intensities and transcript concentration for affymetrix genechip arrays
    • Chudin E, Walker R, Kosaka A, Wu SX, Rabert D, Chang TK, Kreder DE (2002) Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays. Genome Biol 3:RESEARCH0005
    • (2002) Genome Biol , vol.3
    • Chudin, E.1    Walker, R.2    Kosaka, A.3    Wu, S.X.4    Rabert, D.5    Chang, T.K.6    Kreder, D.E.7
  • 31
    • 0141450348 scopus 로고    scopus 로고
    • Comparison and meta-analysis of microarray data: From the bench to the computer desk
    • Moreau Y, Aerts S, De Moor B, De Strooper B, Dabrowski M (2003) Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends Genet 19:570-577
    • (2003) Trends Genet , vol.19 , pp. 570-577
    • Moreau, Y.1    Aerts, S.2    De Moor, B.3    De Strooper, B.4    Dabrowski, M.5
  • 32
    • 0036793318 scopus 로고    scopus 로고
    • Use of rna and genomics dna references for inferred comparisons in dna microarray analyses
    • Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J (2002) Use of RNA and genomics DNA references for inferred comparisons in DNA microarray analyses. Biotechiques 33:924-930
    • (2002) Biotechiques , vol.33 , pp. 924-930
    • Kim, H.1    Zhao, B.2    Snesrud, E.C.3    Haas, B.J.4    Town, C.D.5    Quackenbush, J.6
  • 33
    • 2342624566 scopus 로고    scopus 로고
    • Microarray reality checks in the context of a complex disease
    • Miklos GL, Maleszka R (2004) Microarray reality checks in the context of a complex disease. Nat Biotechnol 22:615-621
    • (2004) Nat Biotechnol , vol.22 , pp. 615-621
    • Miklos, G.L.1    Maleszka, R.2
  • 34
    • 27144548491 scopus 로고    scopus 로고
    • The external rna controls consortium: A progress report
    • The External RNA Controls Consortium
    • The External RNA Controls Consortium (2005) The external RNA controls consortium: a progress report. Nat Methods 2:731-734
    • (2005) Nat Methods , vol.2 , pp. 731-734
  • 36
    • 0035863927 scopus 로고    scopus 로고
    • Assessment of clone identity and sequence fidelity for 1189 image cdna clones
    • Halgren RG, Fielden MR, Fong CJ, Zacharewski TR (2001) Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucleic Acids Res 29:582-588
    • (2001) Nucleic Acids Res , vol.29 , pp. 582-588
    • Halgren, R.G.1    Fielden, M.R.2    Fong, C.J.3    Zacharewski, T.R.4
  • 39
    • 26444454986 scopus 로고    scopus 로고
    • A sequence-based identi fication of the genes detected by probesets on the affymetrix u133 plus 2.0 array
    • Harbig J, Sprinkle R, Enkemann SA (2005) A sequence-based identi fication of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 33:e31
    • (2005) Nucleic Acids Res , vol.33
    • Harbig, J.1    Sprinkle, R.2    Enkemann, S.A.3
  • 41
    • 1342263843 scopus 로고    scopus 로고
    • Guidelines for incorporating non-perfectly matched oligonucleotides into target-speci fic hybridization probes for a dna microarray
    • Lee I, Dombkowski AA, Athey BD (2004) Guidelines for incorporating non-perfectly matched oligonucleotides into target-speci fic hybridization probes for a DNA microarray. Nucleic Acids Res 32:681-690
    • (2004) Nucleic Acids Res , vol.32 , pp. 681-690
    • Lee, I.1    Dombkowski, A.A.2    Athey, B.D.3
  • 45
    • 85083608706 scopus 로고    scopus 로고
    • Affymetrix (b) Whole Transcript (WT) Sense Target Labeling Assay Manual, (c) Alternative Transcript Analysis Methods for Exon Arrays v1.1, (d) Exon Array Background Correction v1.0, (e) Exon Probeset Annotations and Transcript Cluster Groupings v1.0, (f) Gene Signal Estimates from Exon Arrays v1.0, (g) Quality Assessment of Exon Arrays v1.0', HumanExon1.0 ST Array Manuals and White Papers
    • Affymetrix (2005) (a) Exon Array Computational Tool Software User's Guide, (b) Whole Transcript (WT) Sense Target Labeling Assay Manual, (c) Alternative Transcript Analysis Methods for Exon Arrays v1.1, (d) Exon Array Background Correction v1.0, (e) Exon Probeset Annotations and Transcript Cluster Groupings v1.0, (f) Gene Signal Estimates from Exon Arrays v1.0, (g) Quality Assessment of Exon Arrays v1.0', http://www.affymetrix.com/products/arrays/speci fic/exon.affx, Human Exon 1.0 ST Array Manuals and White Papers
    • (2005) Exon Array Computational Tool Software User's Guide
  • 46
    • 34548570202 scopus 로고    scopus 로고
    • Web-based genechip analysis system for large-scale collaborative projects
    • Dai M, Wang P, Jakupovic E, Watson SJ, Meng F (2007) Web-based GeneChip analysis system for large-scale collaborative projects. Bioinformatics 23:2185-2187
    • (2007) Bioinformatics , vol.23 , pp. 2185-2187
    • Dai, M.1    Wang, P.2    Jakupovic, E.3    Watson, S.J.4    Meng, F.5
  • 47
    • 33747520366 scopus 로고    scopus 로고
    • The effect of genechip gene de finitions on the microarray study of cancers
    • Lu X, Zhang X (2006) The effect of GeneChip gene de finitions on the microarray study of cancers. Bioessays 28:739-746
    • (2006) Bioessays , vol.28 , pp. 739-746
    • Lu, X.1    Zhang, X.2
  • 48
    • 33847679625 scopus 로고    scopus 로고
    • Improved precision and accuracy for microarrays using updated probe set de finitions
    • Sandberg R, Larsson O (2007) Improved precision and accuracy for microarrays using updated probe set de finitions. BMC Bioinform 8:48
    • (2007) BMC Bioinform , vol.8 , pp. 48
    • Sandberg, R.1    Larsson, O.2
  • 53
    • 33745476107 scopus 로고    scopus 로고
    • Standardizing the standards
    • Quackenbush J (2006) Standardizing the standards. Mol Syst Biol 2:2006.0010
    • (2006) Mol Syst Biol , vol.2 , Issue.2006 , pp. 0010
    • Quackenbush, J.1
  • 54
    • 66149146644 scopus 로고    scopus 로고
    • Toward a public toxicogenomics capability for supporting predictive toxicology: Survey of current resources and chemical indexing of experiments in geo and arrayexpress
    • Williams-Devane CR, Wolf MA, Richard AM (2009) Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress. Toxicol Sci 109:358-371
    • (2009) Toxicol Sci , vol.109 , pp. 358-371
    • Williams-Devane, C.R.1    Wolf, M.A.2    Richard, A.M.3
  • 55
    • 70249098051 scopus 로고    scopus 로고
    • Postpublication sharing of data and tools
    • CASIMIR Consortium (2009) Postpublication sharing of data and tools. Nature 461:171-173
    • (2009) Nature , vol.461 , pp. 171-173
    • Casimir, C.1
  • 66
    • 0036081355 scopus 로고    scopus 로고
    • Gene expression omnibus: Ncbi gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 67
    • 0347122079 scopus 로고    scopus 로고
    • Cibex: Center for information biology gene expression database
    • Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y (2003) CIBEX: center for information biology gene expression database. C R Biol 326:1079-1082
    • (2003) C R Biol , vol.326 , pp. 1079-1082
    • Ikeo, K.1    Ishi-i, J.2    Tamura, T.3    Gojobori, T.4    Tateno, Y.5
  • 68
    • 33748481775 scopus 로고    scopus 로고
    • Impact of microarray data quality on genomic data submissions to the fda
    • Frueh F (2006) Impact of microarray data quality on genomic data submissions to the FDA. Nat Biotechnol 24:1105-1107
    • (2006) Nat Biotechnol , vol.24 , pp. 1105-1107
    • Frueh, F.1
  • 69
    • 33846703052 scopus 로고    scopus 로고
    • Global clinical data interchange standards are here!
    • Souza T, Kush R, Evans JP (2007) Global clinical data interchange standards are here! Drug Discov Today 12:174-181
    • (2007) Drug Discov Today , vol.12 , pp. 174-181
    • Souza, T.1    Kush, R.2    Evans, J.P.3
  • 70
    • 85083614291 scopus 로고    scopus 로고
    • U.S. Environmental Protection Agency DRAFT: Interim Guidance for Microarray-Based Assays: Data Submission, Quality, Analysis, Management, and Training Considerations
    • U.S. Environmental Protection Agency DRAFT: Interim Guidance for Microarray-Based Assays: Data Submission, Quality, Analysis, Management, and Training Considerations (2007). http://www.epa.gov/osa/spc/pdfs/epa-interim- guidance-for-microarray-based-assays-external-review-draft.pdf
    • (2007)


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.