Bioinformatics Advance Access published online on April 10, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn134
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Towards patterns tree of gene co-expression in eukaryotic species
1School of Life Science and Technology, Tongji University, Shanghai 200092, China
2 Institution of Chinese and Western Medcine Integration, Huashan Hospital, Fudan University, Shanghai 200040, China
3Department of Bioinformatics, Harbin Medical University, Harbin 150086, China
4Institute of Medical Technology, University of Tampere, Tampere 33014, Finland
*To whom correspondence should be addressed. Haiyun Wang, E-mail: whywhy_flying{at}163.com, Qi Wang, E-mail: wtq_flying{at}hotmail.com
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Abstract |
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Motivation: Cellular pathways behave coordinated regulation activity, and some reported works also have affirmed that genes in the same pathway have similar expression pattern. However, the complexity of biological systems regulation actually causes expression relationships between genes to display multiple patterns, such as linear, nonlinear, local, global, linear with time-delayed, nonlinear with time-delayed, monotonic and non-monotonic, which should be the explicit representation of cellular inner regulation mechanism in mRNA level. To investigate the relationship between different patterns, our work aims to systematically reveal gene expression relationship patterns in cellular pathways and to check for the existence of dominating gene expression pattern. By a large scale analysis of genes expression in three eukaryotic species, Saccharomyces cerevisiae, Caenorhabditis elegans and Human, we constructed gene co-expression patterns tree to systematically and hierarchically illustrate the different patterns and their interrelations.
Results: The results show that the linear is the dominating expression pattern in the same pathway. The time-shifted pattern is another important relationship pattern. Many genes from the different pathway also present co-expression patterns. The nonlinear, non-monotonic and time-delayed relationship patterns reflect the remote interactions between the genes in cellular processes. Gene co-expression phenomena in the same pathways are diverse in different species. Genes in Saccharomyces cerevisiae and Caenorhabditis elegans present strong co-expression relationships, especially in Caenorhabditis elegans, co-expression is more universal and stronger due to its special array of genes. However in Human, gene co-expression is not apparent and the human genome involves more complicated functional relationships. In conclusion, different patterns corresponding to different coordinating behaviors coexist. The patterns trees of different species give us comprehensive insight and understanding of genes expression activity in the cellular society.
Contact: whywhy_flying{at}163.com; wtq_flying{at}hotmail.com
Associate Editor: Dr. Trey Ideker
#The authors contributed equally to this work
Received on January 26, 2008; revised on April 8, 2008; accepted on April 9, 2008
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