Functional Comparison of Microarray Data Across Multiple Platforms Using the Method of Percentage of Overlapping Functions
Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.
Key wordsMicroarray Biological pathway database Functional comparison Percentage of overlapping functions R Gene expression
The authors would like to thank Drs. Minjun Chen and Zhihua Xu in Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration for their enlightening comments and hearty discussions in reviewing the manuscript, and Dr. Lin Xie in Department of Aquaculture and Fisheries, University of Arkansas at Pine Bluff for her advice on the statistical methods used in this manuscript. The views presented in this chapter do not necessarily reflect those of the Food and Drug Administration.
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