Microarray RNA transcriptional profiling: Part II. Analytical considerations and annotation

Expert Review of Molecular Diagnostics

Volumn 6, Issue 5, 2006, Pages 703-715

  Ahmed, Farid E ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

Analysis; Bioinformatics; Databases; Statistics; Transformation; Validation

Indexed keywords

DATA ANALYSIS; DATA BASE; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC PROCEDURES; INFORMATION PROCESSING; INFORMATION SCIENCE; MICROARRAY ANALYSIS; REVIEW; RNA TRANSCRIPTION; RNA TRANSCRIPTION PROFILING MICROARRAY; VALIDATION PROCESS;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, COMPLEMENTARY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 33746828379     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.6.5.703     Document Type: Review

References (100)

1. Ahmed FE. I. Microarrays RNA transcriptional profiling: platform, experimental design and standardization. Exp. Rev. Mol. Diag. 6(4), 535-550 (2006).
2. Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 32(Suppl.), 496-501 (2002).
3. Durbin BP, Rocke DM. Variance stabilizing transformation for two-color microarrays. Bioinformatics 20, 660-667 (2004).
4. Qin LX, Kerr KF. Empirical evaluation of data transformation and ranking statistics for microarray analysis. Nucleic Acids Res. 32, 5471-5479 (2004).
5. Konishi T. Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. BMC Bioinformatics 5, 5 (2004).
6. Yang YH, Dudoit S, Luu P et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30, E15 (2002).
7. Ahmed FE. Quantitative real-time RT-PCR: application to cancer. Cancer Genom. Proteom. 2, 317-332 (2005).
8. Lee MLT, Kuo FC, Whitmore GA, Sklar J. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridization. Proc. Natl Acad. Sci USA 97, 9834-9839 (2000).
9. Bilban M, Buchler LK, Head S, Desoye G, Quaranta V. Normalizing DNA microarray data. Curr. Issues Mol. Biol. 4, 57-64 (2002).
10. Cheadle C, Vawter MP, Freed WJ, Becker K. Analysis of microarray data using z-score transformation. J. Mol. Diag. 5, 73-81 (2003).
11. Park T, Yi SG, Kang SH et al. Evaluation of normalization methods for microarray data. BMC Bioinformatics 4, 33 (2003).
12. Cleveland W. Robust locally weighed regression and smoothing scatter lots. J. Am. Stat. Assoc. 74, 829-836 (1979).
13. Drghici S. Data Analysis Tools for DNA Microarrays. Chapman/CRC, Boca Raton, (2003).
14. Delongchamp RR, Velasco C, Razzaghi M, Harris A, Casciano D. Median-of-subsets normalization of intensities for cDNA array data. DNA Cell. Biol. 23, 653-659 (2004).
15. Eckel JE, Gennings C, Therneau TM et al. Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics 21, 1078-1083 (2005).
16. Huber W, von Heydebreck A, Sültmann M, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, S96-S104 (2002).
17. Bird D, Johnstone P, Wilson T. Normalization of microarray data using a spatial mixed model analysis which include splines. Bioinformatics 20, 3196-3205 (2004).
18. Futschik ME, Crompton T. ONLIN: optimized normalization, visualization and quality testing of two-channel microarray data. Bioinformatics 21, 1724-1726 (2005).
19. Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying genes with differential expressin in replicated cDNA microarray experiment. Stat. Sinice. 12, 111-139 (2002).
20. Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental design and low-level analysis of microarray data. Int. Rev. Neurobiology 60, 25-58 (2004).
21. Vinciotti V, Khanin R, D'Alimonte D et al. An experimental evaluation of a loop versus a reference design for two-channel microarrays. Bioinformatics 21, 492-501 (2005).
22. Lu C. Improving the scaling normalization of high-density oligonucleotide GeneChip expression microarray. BMC Bioinformatics 5, 103 (2004).
23. Geller SC, Gregg JP, Hagerman P, Rocke DM. Transformation and normalization of oligiouclotide array data. Bioinformatics 19, 1817-1823 (2003).
24. Schadt E, Li C, Eliss B, Wong WH. Feature extraction and normalization algorithm for high-density oligonucleotide gene expression data. J. Cell. Biochem. 84, 120-125 (2002).
25. Sidorov IA, Hosack DA, Gee D et al. Oligonucleotide microarray data distribution and normalization. Information Sci. 146, 65-71 (2002).
26. Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
27. Ballman KV, Grill DE, Oberg AL, Therneau JM. Faster cyclic loess: normalizing RNA array via linear models. Bioinformatics 20, 2778-2786 (2004).
28. Stoyanova R, Querec TD, Brown TR, Patriotis C. Normalization of single channel DNA array data by principal component analysis. Bioinformatics 20, 1772-1784 (2004).
29. Seo J, Gordish-Dressman H, Hoffman EP. An interactive power analysis toolk for microarray hypothesis testing and generation. Bioinformatics 22, 808-814 (2006).
30. Colantuoni C, Henry G, Zeger S, Pevsner J. SNOMAD (Standardization and Normalization of Microarray Data): web-accessible gene expression data analysis. Bioinformatics 18, 1540-1541 (2002).
31. Nodon R, Shoemaker J. Statistical issues with microarrays: processing and analysis. Trends Genet. 18, 265-271 (2002).
32. Reimers M. Statistical analysis of microarray data. Addiction Biol. 10, 23-35 (2005).
33. Hyduke DR, Rohlin L, Kao KC, Liao JC. A software package for cDNA microarray data normalization and assessing confidence intervals. OMICS 7, 227-237 (2003).
34. Hochberg Y, Sharper A. Boneferroni procedure for multiple tests of significance. Biometrika 75, 800-803 (1998).
35. Šidák Z. Rectangular confidence regions for the means of multivariate normal distribution. J. Am. Stat. Assoc. 62, 626-633 (1967).
36. Pavlidis P. Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31, 282-289 (2003).
37. Rocke DM, Durbin B. A model for measurement error for gene expression arrays. J. Comput. Biol. 8, 557-569 (2001).
38. Hautamemi S, Edgren H, Vesanen P et al. A novel strategy for microarray quality control using Bayesian networks. Bioinformatics 19, 2031-2038 (2003).
39. Hein AMK, Richardson S, Causton HC, Ambler GK, Green PJ. BGX: a full Bayesian integrated approach to the analysis of Affymetrix GeneChip data. Biostatistics 6, 349-373 (2005).
40. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA 100, 9440-9445 (2003).
41. Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19, 368-375 (2003).
42. Taylor J, Tibshirani R, Efron B. The 'miss rate' for the analysis of gene expression data. Biostatistics 6, 111-117 (2005).
43. Pawitan Y, Michiels S, Koscielny S, Gusnato A, Polner A: false discovery rate, sensitivity and sample size for microarray studies. Bioinformatics 21, 3017-3024 (2005).
44. Efron B, Tibshirani R. Empirical bayes methods and false discovery rates for microarrays. Genet. Epidemiol. 23, 70-86 (2002).
45. Kerr MK, Churchill GA. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc. Natl Acad. Sci. USA 98, 8961-8965 (2001).
46. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121 (2001).
47. Liu WM, Mei R, Di X et al. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18, 1593-1599 (2002).
48. Zhou Y, Abagyan R. Match-only integral distribution (MOID) algorithm for the high-density oligonucleotide array analysis. BMC Bioinformatics 3, 3 (2002).
49. Zhijin W, Irizarry R. Processing of oligonucleotide array data. Nat. Biotechnol. 6, 656-658 (2004).
50. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863-14868 (1988).
51. Shannon W, Culverhouse R, Duncan J. Analyzing microarray data using cluster analysis. Pharmacogenomics 4, 41-51 (2003)
52. Hess KR, Zhang W, Baggerly KA, Stivers DN, Coombers KV. Microarrays: handling the deluge of data and extracting reliable information. Trend Biotechnol. 19, 463-468 (2001).
53. Gollub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer. Class discovery and class prediction by gene expression monitoring. Science 268, 531-537 (1999).
54. Drãghici S. Data Analysis Tools for DNA Microarrays. Chapman/CRC, Boca Raton, (2003).
55. Romualdi C, Vitulo N, Favero MD, Lanfranchi G. MIDAW: a web tool for statistical analysis of microarray data. Nucleic Acids Res. 33, 10.1093/nar/gki497 (2005).
56. Hokamp K, Roche FM, Acab M et al. ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res. 32, 10.1993/nar/gkh446 (2004).
57. Psarros M, Heber S, Sick M et al. RACE: remote analysis computation for gene expression data. Nucleic Acids Res. 33, 10.1093/nar/gki490 (2005).
58. Dudoit S, Gentleman RC, Quackenbush J. Open source software for the analysis of microarray data. BioTechnique 34(Suppl.), 45-51 (2003).
59. Ahmed FE. Development of novel diagnostic and prognostic molecular marker for sporadic colon cancer. Exp. Rev. Mol. Diag. 5, 337-352 (2005).
60. Gardiner-Garden M, Littlejohn TG. A comparison of microarray databases. Brief. Bioinf. 2, 143-157 (2001).
61. Ball CA, Awad IAB, Demeter J et al. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 33, 10.1093/nar/gki006 (2005).
62. Karolchik D, Hinrichs AS, Furey TS et al. The UCSF Table Browser data retrieval tool. Nucleic Acids Res. 32, 10.1093/nar/gkh103 (2004).
63. Manduchi E, Grant GR, He H et al. RAD and the RAD study-Annotator: an approach to collection, organization and exchange of all relevant information for high throughput gene expression studies. Bioinformatics 20, 452-459 (2004)
64. Stoeckert CJ Jr, Caaston HC, Ball CA. Microarray databases: standards and ontologies. Nat. Genet. 32, 469-473 (2002).
65. Parkinson H, Sarkans U, Shojatalab M et al. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 33, 10.1093/nar/gki056 (2005).
66. Wheeler DL, Church DM, Edgar R et al. Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 32, 1001093/nar/gkh073 (2004).
67. Ikeo K, Ishi J, Tamura T, Gojobori T, Tateno Y. CIBEX: Center for Information Biology gene Expression database. C. R. Biologie 326, 1079-1082 (2003).
68. Kapushesky M, Kemmeren P, Culhane AC et al. Expression Profiler: next generation - an online platform analysis of microarray data. Nucleic Acids Res. 32, 0.1093/nar/gkh470 (2004).
69. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
70. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene gene-oriented information at NCBI. Nucleic Acids Res. 33, D54-D58 (2005).
71. Ashburner M, Ball CA, Blike JA et al. Gene ontology tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 (2000).
72. Doniger SW, Salomonis N, Dahlquist KD et al. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4, R7 (2003).
73. Lee HK, Braynen W, Keshav K, Pavlidis P. ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6, 269 10.1186/1471-2105-6-269 (2005).
74. Harris MA, Clark J, Ireland A et al. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, 10.1093/nar/gkh036 (2004).
75. Drghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA. Global functional profiling of gene expression. Genomics 81, 98-104 (2003).
76. Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Drghici S. Recent additions and improvements to the Onto-Tools. Nucleic Acids Res. 33, 10.1093/nar/gki472 (2005).
77. Drghici S, Khatri P, Shah A, Tainsky MA Assessing the functional bias of commercial microarrays using the ontocompare database. BioTechniques 34, 55-61 (2003).
78. Brazma A, Vilo J. Gene expression data analysis. FEBS Lett. 480, 17-24 (2000).
79. Butte A. The use and analysis of microarray data. Nature Rev. Drug Discovery 1, 951-960 (2002).
80. Riva A, Carpentier AS, Torrésani B, Hénaut A. Comments on selected fundamental aspects of microarray analysis. Comput. Biol. Chem. 29, 319-336 (2005).
81. http://itb.biologie.huberlin.de~futschik/software/ROLIN
82. Bioconductor www.bioconductor.org
83. Human Conmputer Interaction Lab www.cs.umd.edu/hcil/hce
84. National Caner Institute - Biometric Research Branch http://Linus.nci. nih.gov/BRB-ArrayTools
85. Standarization and Normalization of Microarray Data http://pevsnerlab. kennedykrieger.org/snomad.htm
86. http://genomine.org/qvalue/
87. Home page of Yoav Benjamini www.math.tau.ac.il/~ybenja
88. www.stat.stanford.edu/tibs/SAM/index.html.
89. Open-source software for bioinformatics www.bioconductor.org
90. The Institute for Genomic Research www.tigr.org/software
91. BioArray Software Environment http://base.thep.lu.se
92. www.ebl.ac.uk/arrayexpress
93. European Bioinformatics Institute www.ebi.ac.uk/expressionprofiler
94. Center for Information Biology gene EXpression database http://cibex.nig.ac.jp
95. National Center for Biotechnology Information Gene Expression Omnibus www.ncbi.nlm.nih.gov/geo
96. Gene Ontology Database www.geneontology.org/
97. Gene Ontology Software and Databases www.godatabase.org/dev
98. Gene map annotator and pathway profiler www.GenMAPP.org
99. http://microarray.cu.genome.org
100. Intelligent systems and bioinformatics library http://vortex.cs.wayne. edu/Projects.html