Review and Overview

Selected Articles

Microarray Related Reference Sites/Links

[review and overview]

Nature Genetics published a series called Chipping Forcast with several pertinent review articles relating to the evolution of microarray technology, analysis and experimental design:

Chipping Forecast (January 1999)

Chipping Forecast II (December 2002)

Chipping Forecast III (June 2005)

Allison DB, Cui X, Page GP, Sabripour M. (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet., 7: 55-65. [PubMed]

Khatri P, Draghici S. (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics., 21: 3587-3595. [PubMed]

Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W. (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods., 2: 345-350. [PubMed]

Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP (2004) A benchmark for Affymetrix GeneChip expression measures. Bioinformatics., 12: 323-331. [PubMed]

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., 10: 570-577. [PubMed]

Bolstad BM, Irizarry RA, Astrand M, Speed TP. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics., 19: 185-193. [PubMed]

Slonim DK. (2002) From patterns to pathways: gene expression data analysis comes of age. Nat Genet., 32: 502-508. [PubMed]

Butte A. (2002) The use and analysis of microarray data. Nat Rev Drug Discov, 1: 951-960. [PubMed]

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet., 29: 365-371. [PubMed]

Quackenbush J (2001) Computational analysis of microarray data. Nat Rev Genet, 6: 418-427. [PubMed]

Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature, 405: 827-836. [PubMed]

Bassett DE Jr, Eisen MB, Boguski MS (1999) Gene expression informatics--it's all in your mine. Nat Genet, 21: 51-55. [PubMed]

Brown PO, Botstein D (1999) Exploring the new world of the genome with DNA microarrays. Nat Genet, 21: 33-37. [PubMed]

Zhang MQ (1999) Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Res, 9: 1156. [PubMed]

Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286: 531-537. [PubMed]

Eisen M, Spellman PT, Brown PO and Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA, 95: 14863-14868. [PubMed]

[selected articles]

Two related portals at nature.com contain an updated collection of recent nature articles related to gene and protein expression analysis:

Web Focus on Microarrays

The Omics Gateway

Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433: 769-73. [PubMed]

Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. (2004) Large-scale copy number polymorphism in the human genome. Science, 305: 525-528. [PubMed]

van den Oord EJ, Sullivan PF. (2003) False discoveries and models for gene discovery. Trends Genet., 19: 537-542. [PubMed]

Dyrskjot L, Thykjaer T, Kruhoffer M, Jensen JL, Marcussen N, Hamilton-Dutoit S, Wolf H, ORntoft TF. (2003) Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet, 33: 90-96. [PubMed]

Aach J, Church GM (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics, 17: 495-508. [PubMed]

Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Global Analysis of Protein Activities Using Proteome Chips. Science, 293: 2101-2105. [PubMed]

Schulze A, Downward J (2001) Navigating gene expression using microarrays--a technology review. Nat Cell Biol, 3: E190-E195. [PubMed]

Altman RB, Raychaudhuri S (2001) Whole-genome expression analysis: challenges beyond clustering. Curr Opin Struct Biol, 11: 340-347. [PubMed]

Shoemaker DD, Schadt EE, Armour CD, He YD, Garrett-Engele P, McDonagh PD, Loerch PM, Leonardson A, Lum PY, Cavet G, Wu LF, Altschuler SJ, Edwards S, King J, Tsang JS, Schimmack G, Schelter JM, Koch J, Ziman M, Marton MJ, Li B, Cundiff P, Ward T, Castle J, Krolewski M, Meyer MR, Mao M, Burchard J, Kidd MJ, Dai H, Phillips JW, Linsley PS, Stoughton R, Scherer S, Boguski MS (2001) Experimental annotation of the human genome using microarray technology. Nature, 409: 922-927. [PubMed]

Lee ML, 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. [PubMed]

Getz G, Levine E, Domany E (2000) Coupled two-way clustering analysis of gene microarray data. Proc Natl Acad Sci USA, 97: 12079-12084. [PubMed]

Brown CS, Goodwin PC, Sorger PK (2001) Image metrics in the statistical analysis of DNA microarray data. Proc Natl Acad Sci USA, 98: 8944-8949. [PubMed]

Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA, 98: 31-36. [PubMed]

Schadt EE, Li C, Su C, Wong WH (2001) Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem, 80: 192-202. [PubMed]

Baggerly KA, Coombes KR, Hess KR, Stivers DN, Abruzzo LV, Zhang W (2001) Identifying differentially expressed genes in cDNA microarray experiments. J of Comp Biol, 8: 639-659. [PubMed]

Kerr MK, Churchill GA (2001) Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc Natl Acad Sci USA, 98: 8961-8965. [PubMed]

Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem , 276: 19937-19944. [PubMed]

Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res , 61: 5979-5984. [PubMed]

Claverie J (1999) Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet, 8: 1821-1832. [PubMed]

Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS (1998) Data management and analysis for gene expression arrays. Nat Genet , 20: 19-23. [PubMed]

[microarray related reference sites]

Below is a list of links to other sites referencing updated microarray analysis information/references:

Web Focus on Microarrays (Nature Reviews)

Web Focus on Human Genomics (Nature.com)

Bibliography on Microarray Data Analysis (maintained by Wentian Li at North Shore LIJ Research Institute)

Microarray Resources e-library (at array-it.com)