Bioinformatics Advance Access originally published online on April 10, 2008
Bioinformatics 2008 24(11):1367-1373; doi:10.1093/bioinformatics/btn134
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Towards patterns tree of gene coexpression in eukaryotic species
1School of Life Science and Technology, Tongji University, Shanghai 200092, 2Institute of Chinese Traditional Medicine and Western Medicine Integration, Huashan Hospital, Fudan University, Shanghai 200040, 3Department of Bioinformatics, Harbin Medical University, Harbin 150086, China, 4Center for Systems Biology, Soochow University, Suzhou 215006, China and 5Institute of Medical Technology, University of Tampere, Tampere 33014, Finland
*To whom correspondence should be addressed.
 |
Abstract |
|---|
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, non-linear, local, global, linear with time-delayed, non-linear 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 coexpression 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 coexpression patterns. The non-linear, non-monotonic and time-delayed relationship patterns reflect the remote interactions between the genes in cellular processes. Gene coexpression phenomena in the same pathways are diverse in different species. Genes in S.cerevisiae and C.elegans present strong coexpression relationships, especially in C.elegans, coexpression is more universal and stronger due to its special array of genes. However in Human, gene coexpression 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
Supplementary information: Supplementary data are available at Bioinformatics online.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Received on January 26, 2008; revised on April 8, 2008; accepted on April 9, 2008
CiteULike 
Connotea 
Del.icio.us What's this?