Research article

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

Murat Cankaya^1,2 , Ana Martinez Hernandez¹ , Mehmet Ciftci² , Sukru Beydemir² , Hasan Ozdemir² , Harun Budak^1,2 , Ilhami Gulcin² , Veysel Comakli² , Tufan Emircupani² , Deniz Ekinci² , Muslum Kuzu² , Qiuhong Jiang¹ , Gregor Eichele¹ and Omer Irfan Kufrevioglu²

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

author email corresponding author email

BMC Genomics 2007, 8:232doi: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.