Selected References on Microarray Analysis

Microarray Review Articles

1. Brady, G. (2000) Expression profiling of single mammalian cells — small is beautiful. Yeast 17:211-217.
   
   
2. Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Lee SN, and Quackenbush J. (2000) A concise guide to cDNA microarray analysis. BioTechniques 29: 548-562.
   
   Protocols for designing PCR clones, microarray printing, labeling of probe and hybridization to the microarrays. This article also provides an insight into data normalization and analysis.
   
   
3. Scheidl SJ, Nilsson S, Kalén M, Hellström M, Takemoto M, Håkansson J, and Lindahl P. (2002) mRNA Expression Profiling of Laser Microbeam Microdissected Cells from Slender Embryonic Structures. Am J Pathol 160:801-813.
   
   
4. Schulze A, and Downward J. (2001) Navigating gene expression using microarrays — a technology review. Nature Cell Biology 3:E190-E195.
   
   
5. Siedow JN. (2001) Making sense of microarrays. Genome Biology 2(2): Reports 4003.
   
   
6. Van Berkum NL, Holstege FC. (2001) DNA microarrays: raising the profile. Curr Opin Biotechnol 12(1):48-52.
   
   Designing microarray experiments and analyzing microarray data.
   

Microarray Articles of Interest

1. Baldwin D, Crane V, and Rice D. (1999) A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants. Current Opinion in Plant Biology 2:96-103.
   
   
2. Dorris DR, Ramakrishnan R, Trakas D, Dudzik F, Belval R, Zhao C, Nguyen A, Domanus M, and Mazumder A. (2002) A Highly Reproducible, Linear, and Automated Sample Preparation Method for DNA Microarrays. Genome Research 12:976–984.
   
   
3. Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Gostwick DG, Brown MR, Buetow KH, et al. (2000) Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications. J Mol Diagnostics 2:60-65.
   
   
4. Lee M-LT, Kuo FC, Whitmore GA, Sklar J. (2000) Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 97:9834-9839.
   
   
5. Leemans R, Egger B, Loop T, Kammermeier L, He H, Hartmann B, Certa U, Hirth F, and Reichert H. (2000) Quantitative transcript imaging in normal and heat-shocked Drosophila embryos by using high-density oligonucleotide arrays. Proc Natl Acad Sci USA 97:12138-12143.
   
   
6. *Lee PD, Sladek R, Greenwood CMT, and Hudson HJ. (2001) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Research 12:292-297.
   
   
7. Li F, and Stormo GD (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17(11): 1067-1076.
   
   Discusses algorithms to select oligonucleotides from genes or open reading frames and to understand their hybridization behavior.
   
   
8. Luo L, Salunga RC, Guo H, Bittner A, You KC, Galindo JE, Xiao H, Rogers KE, Wan JS, Jackson MR, and Erlander MG. (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nature Medicine 5:117-122.
   
   
9. Luzzi V, Holtschlag V, and Watson MA. (2001) Expression profiling of ductal carcinoma in situ by laser capture microdissection and high-density oligonucleotide arrays. Am J Pathol 158:2005-2010.
   
   Makes good use of RNA controls for evaluating two rounds of amplification.
   
   
10. *Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge Ø, Pergamenschikov A, Willimas C, Zhu SX, Lønning PE, Børresen-Dale A-L, Brown PO, and Botstein D. (2000) Molecular Portraits of human breast tumours. Nature 406:747-752.
    
    One of the first papers to show that gene expression profiles can be used to categorize human tumors into distinct subgroups.
    
    
11. Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, and Church GM. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nature Biotechnology 18:1262-1268.
    
    
12. Sørlie T, Perou CM, Tibshirani R, Aas R, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lønning PE, and Børresen-Dale A-L. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98:10869-10874.
    
    
13. Wei Y, Lee J-M, Richmond C, Blattner FR, Rafalski JA, and LaRossa RA. (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183:545-556.
    
    
14. Wildsmith SE, Archer GE, Winkley AJ, Lane PW, and Bugelski PJ. (2001) Maximization of signal derived from cDNA microarrays. BioTechniques 30: 202-208.
    
    Uses a classical statistical method to assess the experimental factors that contribute to variability in a microarray experiment.
    
    
15. *Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttal RL, Stack R, Becker JW, Montgomery JR, Vainer M, and Johnston R. (2001) An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. Nuc. Acids. Res. 29(8): e41.
    
    A detailed analysis of the reproducibility of cDNA microarray experiments in determining differential mRNA expression.
    
    
16. Zarrinkar PP, Mainquist JK, Zamora M, Stern D, Welsh JB, Sapinosa LM, Hampton GM, and Lockhart DJ. (2001) Arrays of arrays for high-throughput gene expression profiling. Genome Research 11:1256-1261.
    

Verification of Gene Array Results

1. Rajeevan MS, Vernon SD, Taysavang N, and Unger ER. (2001) Validation of array-based gene expression profiles by real-time (kinetic) RT-PCR. Journal of Molecular Diagnostics 3(1): 26-31.
   
   The use of a real-time RT-PCR method, using SYBR Green I detection and Tm analysis, to verify microarray results.
   
   
2. Pradet-Balade B, Boulmé F, Müllner EW, and Garcia-Sanz JA. (2001) Reliability of mRNA Profileing: Verification for Samples with Different Complexities. BioTechniques 31:1352-1357.
   

Web Sites Containing Microarray Information

1. Free probe and gene information
   http://www.affymetrix.com
   http://www.stat.berkeley.edu/users/terry/zarray/Html/index.html
   
   
2. Additional papers on microarray analysis
   http://linkage.rockefeller.edu/wli/microarray/
   
   
3. Microarray resources, including links to papers, companies, newsgroups, software, introductory information, and individual lab web sites: http://www.deathstarinc.com/science/biology/chips.html
   
   
4. Pat Brown's web page includes protocols and a microarray forum:
   http://cmgm.stanford.edu/pbrown/

Articles on Instrumentation and Software Analysis

1. Brush M. (2001) Making Sense of Microchip Array Data. The Scientist 15(9): 25. (Full text)
   
   Information on microarray software analysis packages.
   
   
2. Cortese JD. (2000) Array of options. The Scientist 14(11): 26. (Full text)
   
   Information on companies making instruments for microarray production and analysis.
   
   
3. Lee, JK. (2001) Analysis Issues for Gene Expression Array Data. Clinical Chemistry 47(8): 1350-1352.
   
   The truth about three common misconceptions regarding array experiments.

Papers on aRNA Amplification

1. *Baugh LR, Hill AA, Brown EL, and Hunter CP. (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nuc. Acids. Res. 29(5): e29.
   
   Meticulously dissects the steps of the Eberwine RNA amplification protocol to find those that affect the linearity of amplification and yield of amplified RNA. It also analyzes the statistical variations, 3' bias, linearity of amplification and sequence-dependent biases observed with the technique.
   
   
2. Kacharmina EJ, Crino PB, and Eberwine JH. (1999) Preparation of cDNA from single cells and subcellular regions. Methods in Enzymology 303: 3-19.
   
   A review describing the Eberwine RNA amplification technique.
   
   
3. Poirier GM-C, and Erlander MG. (1998) Postdifferential Display: parallel processing of candidates using small amounts of RNA. Methods: A companion to methods of Enzymology 16:444-452.
   
   A 96-well plate format for making cDNA probes from amplified RNA for differential display analysis.
   
   
4. Van Gelder RN, Von Zastrow ME, Yool A, Dement WC, Barchas JD, and Eberwine JH. (1990) Amplified RNA synthesized from limited quantities of heterogenous cDNA. Proc. Natl. Acad. Sci. USA 87:1663-1667.
   
   The original paper by Eberwine describing the antisense RNA (aRNA) amplification procedure.
   
   
5. Wang E, Miller LD, Ohnmacht GA, Liu ET, and Marincola FM. (2000) High-fidelity mRNA amplification for gene profiling. Nature Biotechnology 18:457-459.
   
   Presents a modified Eberwine RNA amplification protocol that uses a template switch method to eliminate 3' bias.

Applications of the Eberwine RNA Amplification Protocol

1. Luo L, Salunga RC, Guo H, Bittner A, Joy KC, Galindo JE, Xiao H, Rogers KE, Wan JS, Jackson MR, and Erlander MG. (1999) Gene expression profiles of laser-captured adjacent neuronal subtypes. Nature Medicine 5(1):117-122. (Full text)
   
   Interesting fusion of laser capture microdissection (LCM) and the aRNA amplification technique to assess the gene expression profiles of neighboring neurons.
   
   
2. O'Dell DM, Ragupathi R, Crino PB, Morrison III B, Eberwine JH, and McIntosh TK (1998) Amplification of mRNAs from Single, Fixed, TUNEL-positive cells. BioTechniques 25(4): 566-568.

*Recommended reading for anyone interested in doing microarray analysis.

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