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KMID : 0613820160260080904
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Journal of Life Science
2016 Volume.26 No. 8 p.904 ~ p.910
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Construction of Gene Network System Associated with Economic Traits in Cattle
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Lim Da-Jeong
Kim Hyung-Yong
Cho Yong-Min
Chai Han-Ha
Park Jong-Eun
Lim Kyu-Sang
Lee Seung-Soo
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Abstract
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Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The gene network analysis has been performed by diverse types of methods such as gene co-expression, gene regulatory relationships, protein-protein interaction (PPI) and genetic networks. Moreover, the network-based methods were described for predicting gene functions such as graph theoretic method, neighborhood counting based methods and weighted function. However, there are a limited number of researches in livestock. The present study systemically analyzed genes associated with 102 types of economic traits based on the Animal Trait Ontology (ATO) and identified their relationships based on the gene co-expression network and PPI network in cattle. Then, we constructed the two types of gene network databases and network visualization system (http://www.nabc.go.kr/cg). We used a gene co-expression network analysis from the bovine expression value of bovine genes to generate gene co-expression network. PPI network was constructed from Human protein reference database based on the orthologous relationship between human and cattle. Finally, candidate genes and their network relationships were identified in each trait. They were typologically centered with large degree and betweenness centrality (BC) value in the gene network. The ontle program was applied to generate the database and to visualize the gene network results. This information would serve as valuable resources for exploiting genomic functions that influence economically and agriculturally important traits in cattle.
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KEYWORD
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Cattle, Gene co-expression network, potein-protein network, web database
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