Abstract
BackgroundMicroarray gene expression data are accumulating in public databases. The expression profiles contain valuable information for understanding human gene expression patterns. However, the effective use of public microarray data requires integrating the expression profiles from heterogeneous sources.ResultsIn this study, we have compiled a compendium of microarray expression profiles of various human tissue samples. The microarray raw data generated in different research laboratories have been obtained and combined into a single dataset after data normalization and transformation. To demonstrate the usefulness of the integrated microarray data for studying human gene expression patterns, we have analyzed the dataset to identify potential tissue-selective genes. A new method has been proposed for genome-wide identification of tissue-selective gene targets using both microarray intensity values and detection calls. The candidate genes for brain, liver and testis-selective expression have been examined, and the results suggest that our approach can select some interesting gene targets for further experimental studies.ConclusionA computational approach has been developed in this study for combining microarray expression profiles from heterogeneous sources. The integrated microarray data can be used to investigate tissue-selective expression patterns of human genes.
Highlights
Microarray gene expression data are accumulating in public databases
The results further suggest that the publicly available microarray expression profiles from heterogeneous sources can be integrated into a single dataset for examining gene expression patterns across various tissues
These expression profiles have been combined into a single dataset after global normalization, and used for the genome-wide analysis of tissue-selective gene expression
Summary
Microarray gene expression data are accumulating in public databases. The effective use of public microarray data requires integrating the expression profiles from heterogeneous sources. There are many different types of cells in the human body, and similar cells group together to form a tissue with a specialized function. Certain genes are expressed or preferentially in a particular tissue. These genes are broadly called tissue-selective genes [1]. Note that tissue specificity is regarded as a special case of tissue selectivity, and tissue-specific genes are expressed only in a particular tissue. It is a fundamental question in biology to understand how selective gene expression underlies
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