Campus Units
Electrical and Computer Engineering, Virtual Reality Applications Center, Bioinformatics and Computational Biology
Document Type
Article
Publication Version
Published Version
Publication Date
10-21-2009
Journal or Book Title
BMC Bioinformatics
Volume
10
First Page
346
DOI
10.1186/1471-2105-10-346
Abstract
Background
Biological networks characterize the interactions of biomolecules at a systems-level. One important property of biological networks is the modular structure, in which nodes are densely connected with each other, but between which there are only sparse connections. In this report, we attempted to find the relationship between the network topology and formation of modular structure by comparing gene co-expression networks with random networks. The organization of gene functional modules was also investigated.
Results
We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by using 1094 microarrays. We then analyzed the topological properties of AGCN and partitioned the network into modules by using an efficient graph clustering algorithm. In the AGCN, 382 hub genes formed a clique, and they were densely connected only to a small subset of the network. At the module level, the network clustering results provide a systems-level understanding of the gene modules that coordinate multiple biological processes to carry out specific biological functions. For instance, the photosynthesis module in AGCN involves a very large number (> 1000) of genes which participate in various biological processes including photosynthesis, electron transport, pigment metabolism, chloroplast organization and biogenesis, cofactor metabolism, protein biosynthesis, and vitamin metabolism. The cell cycle module orchestrated the coordinated expression of hundreds of genes involved in cell cycle, DNA metabolism, and cytoskeleton organization and biogenesis. We also compared the AGCN constructed in this study with a graphical Gaussian model (GGM) based Arabidopsis gene network. The photosynthesis, protein biosynthesis, and cell cycle modules identified from the GGM network had much smaller module sizes compared with the modules found in the AGCN, respectively.
Conclusion
This study reveals new insight into the topological properties of biological networks. The preferential hub-hub connections might be necessary for the formation of modular structure in gene co-expression networks. The study also reveals new insight into the organization of gene functional modules.
Rights
© 2009 Mao et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
Mao et al
Copyright Date
2009
Language
en
File Format
application/pdf
Recommended Citation
Mao, Linyong; Van Hemert, John L.; Dash, Sudhansu; and Dickerson, Julie A., "Arabidopsis gene co-expression network and its functional modules" (2009). Electrical and Computer Engineering Publications. 83.
https://lib.dr.iastate.edu/ece_pubs/83
Comments
This article is from BMC Bioinformatics 10 (2009): 346. Posted with permission.