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

Murat Cankaya,Veysel Comakli,Tufan Emircupani,Mehmet Ciftci,Deniz Ekinci,Muslum Kuzu,Harun Budak,Qiuhong Jiang,Hasan Ozdemir,Omer Irfan Kufrevioglu,Ana Martinez Hernandez,Sukru Beydemir,Gregor Eichele,Ilhami Gulcin

doi:10.1186/1471-2164-8-232

Murat Cankaya, Veysel Comakli + Show 12 more

Open Access

https://doi.org/10.1186/1471-2164-8-232

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Abstract

BackgroundIn 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.ResultsThe 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.ConclusionThe 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.

Highlights

In situ hybridization (ISH) is a powerful method for visualizing gene expression patterns at the organismal level with cellular resolution
Expression patterns of mouse genes encoding proteins with catalytic activity Under its "Molecular Function" category, Gene Ontology lists approximately 2700 gene products that exhibit activity associated with catalysis [22]
Genes were selected on the basis of three not mutually exclusive criteria: (1) the genes scored as 'present' in a duplicate Affymetrix microarray chip (MA) hybridized with mRNA from E14.5 mouse embryos (MA data were deposited at NCBI GEO under accession number GSE6081); (2) all gene products encoding glycolytic and TCA cycle enzymes were selected; (3) for kinases, the intensity of the MA signal was ranked by the raw numerical value, and the 190 most stronglyexpressed transcripts were selected

Summary

Introduction

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. When and where genes are expressed provides useful information about their function. This view forms the basis of several genome-scale projects that attempt the systematic localization of mRNAs and/or proteins expressed in tissues and cells [1,2]. Expression sites are annotated and images are made accessible on a public website [3,4]

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