[Frontiers in Bioscience E2, 325-338, January 1, 2010]

[Frontiers in Bioscience E2, 325-338, January 1, 2010]

Microarray probes and probe sets

Hongfang Liu, Ionut Bebu, Xin Li

Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC, 20007, USA

TABLE OF CONTENTS

1. Abstract
2. Introduction
2. Introduction
3. Microarray probes and probe sets: 3.1. cDNA microarrays; 3.2. Oligonucleotide microarrays; 3.3. Tools for probe selection
4. Redefinition of Affymetrix chips: 4.1. Issues related to Affymetrix probes; 4.2. Tools, resources, and studies using Affymetrix probe sequence data; 4.3. Statistics of Affymetrix probes
5. Comparison analysis of different redefinition methods: 5.1. Redefinition used; 5.2. Data set; 5.3. Consistency assessment; 5.4. Comparison outcome
6. Conclusion
7. Acknowledgement
8. References

1. ABSTRACT

DNA microarrays have gained wide use in biomedical research by simultaneously monitoring the expression levels of a large number of genes. The successful implementation of DNA microarray technologies requires the development of methods and techniques for the fabrication of microarrays, the selection of probes to represent genes, the quantification of hybridization, and data analysis. In this paper, we concentrate on probes that are either spotted or synthesized on the glass slides through several aspects: sources of probes, the criteria for selecting probes, tools available for probe selections, and probes used in commercial microarray chips. We then provide a detailed review of one type of DNA microarray: Affymetrix GeneChips, discuss the need to re-annotate probes, review different methods for regrouping probes into probe sets, and compare various redefinitions through public available datasets.