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Open Access Highly Accessed Research article

An analysis of expression patterns of genes encoding proteins with catalytic activities

Murat Cankaya12, Ana Martinez Hernandez1, Mehmet Ciftci2, Sukru Beydemir2, Hasan Ozdemir2, Harun Budak12, Ilhami Gulcin2, Veysel Comakli2, Tufan Emircupani2, Deniz Ekinci2, Muslum Kuzu2, Qiuhong Jiang1, Gregor Eichele1* and Omer Irfan Kufrevioglu2

Author Affiliations

1 Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany

2 Department of Chemistry, Faculty of Arts and Science, Atatürk University, 25240 Erzurum, Turkey

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BMC Genomics 2007, 8:232  doi:10.1186/1471-2164-8-232

Published: 12 July 2007

Abstract

Background

In situ hybridization (ISH) is a powerful method for visualizing gene expression patterns at the organismal level with cellular resolution. When automated, it is capable of determining the expression of a large number of genes.

Results

The expression patterns of 662 genes that encode enzymes were determined by ISH in the mid-gestation mouse embryo, a stage that models the complexity of the adult organism. Forty-five percent of transcripts encoding metabolic enzymes (n = 297) showed a regional expression pattern. A similar percentage was found for the 190 kinases that were also analyzed. Many mRNAs encoding glycolytic and TCA cycle enzymes exhibited a characteristic expression pattern. The annotated expression patterns were deposited on the Genepaint database and are retrievable by user-defined queries including gene name and sites of expression.

Conclusion

The 662 expression patterns discussed here comprised gene products with activities associated with catalysis. Preliminary analysis of these data revealed that a significant number of genes encoding housekeeping functions such as biosynthesis and catabolism were expressed regionally, so they could be used as tissue-specific gene markers. We found no difference in tissue specificity between mRNAs encoding housekeeping functions and those encoding components of signal transduction pathways, as exemplified by the kinases.