Protocols for Nucleic Acid Analysis by Nonradioactive Probes

Volume 353 of the series Methods in Molecular Biology pp 265-300


An Overview
  • Norman H. LeeAffiliated withDepartment of Functional Genomics, The Institute for Genomic Research
  • , Alexander I. SaeedAffiliated withDepartment of Functional Genomics, The Institute for Genomic Research

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Gene expression microarrays are being used widely to address a myriad of complex biological questions. To gather meaningful expression data, it is crucial to have a firm understanding of the steps involved in the application of microarrays. The available microarray platforms are discussed along with their advantages and disadvantages. Additional considerations include study design, quality control and systematic assessment of microarray performance, RNA-labeling strategies, sample allocation, signal amplification schemes, defining the number of appropriate biological replicates, data normalization, statistical approaches to identify differentially regulated genes, and clustering algorithms for data visualization. In this chapter, the underlying principles regarding microarrays are reviewed, to serve as a guide when navigating through this powerful technology.

Key Words

Amplification ANOVA cDNA clustering dye-swap expression matrix expression vector fluorescence gene expression hierarchical hybridization k-means long oligomers microarrays mRNA oligonucleotides probe RNA target t-test