Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks

Lim, Dajeong; Kim, Nam-Kuk; Park, Hye-Sun; Lee, Seung-Hwan; Cho, Yong-Min; Oh, Sung Jong; Kim, Tae-Hun; Kim, Heebal

doi:10.7150/ijbs.7.992

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Int J Biol Sci 2011; 7(7):992-1002. doi:10.7150/ijbs.7.992 This issue Cite

Research Paper

Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks

Dajeong Lim^1,2*, Nam-Kuk Kim^1,3*, Hye-Sun Park¹, Seung-Hwan Lee¹, Yong-Min Cho⁴, Sung Jong Oh¹, Tae-Hun Kim¹, Heebal Kim^2✉

1. Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea
2. Laboratory of Bioinformatics and Population genetics, Seoul National University, Seoul, Republic of Korea
3. Gyeongnam Provincial Office, National Agricultural products Quality management Service, Busan, Republic of Korea
4. Green growth and future strategy team, Director general for planning and coordination, Rural Development Administration, Suwon, Republic of Korea
* The first two authors should be regarded as joint First Authors.

Citation:

Lim D, Kim NK, Park HS, Lee SH, Cho YM, Oh SJ, Kim TH, Kim H. Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks. Int J Biol Sci 2011; 7(7):992-1002. doi:10.7150/ijbs.7.992. https://www.ijbs.com/v07p0992.htm

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Abstract

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 present study systemically analyzed genes associated with bovine marbling score and identified their relationships. The candidate nodes were obtained using MedScan text-mining tools and linked by protein-protein interaction (PPI) from the Human Protein Reference Database (HPRD). To determine key node of marbling, the degree and betweenness centrality (BC) were used. The hub nodes and biological pathways of our network are consistent with the previous reports about marbling traits, and also suggest unknown candidate genes associated with intramuscular fat. Five nodes were identified as hub genes, which was consistent with the network analysis using quantitative reverse-transcription PCR (qRT-PCR). Key nodes of the PPI network have positive roles (PPARγ, C/EBPα, and RUNX1T1) and negative roles (RXRA, CAMK2A) in the development of intramuscular fat by several adipogenesis-related pathways. This study provides genetic information for identifying candidate genes for the marbling trait in bovine.

Keywords: Protein-Protein Interaction (PPI), Network, Marbling, Bovine, Hanwoo

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APA

Lim, D., Kim, N.K., Park, H.S., Lee, S.H., Cho, Y.M., Oh, S.J., Kim, T.H., Kim, H. (2011). Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks. International Journal of Biological Sciences, 7(7), 992-1002. https://doi.org/10.7150/ijbs.7.992.

ACS

Lim, D.; Kim, N.K.; Park, H.S.; Lee, S.H.; Cho, Y.M.; Oh, S.J.; Kim, T.H.; Kim, H. Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks. Int. J. Biol. Sci. 2011, 7 (7), 992-1002. DOI: 10.7150/ijbs.7.992.

NLM

CSE

Lim D, Kim NK, Park HS, Lee SH, Cho YM, Oh SJ, Kim TH, Kim H. 2011. Identification of Candidate Genes related to Bovine Marbling using Protein-Protein Interaction Networks. Int J Biol Sci. 7(7):992-1002.

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