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

Research Paper

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

Dajeong Lim1,2*, Nam-Kuk Kim1,3*, Hye-Sun Park1, Seung-Hwan Lee1, Yong-Min Cho4, Sung Jong Oh1, Tae-Hun Kim1, Heebal Kim2✉

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.

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

This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See http://ivyspring.com/terms for full terms and conditions.
How to cite this article:
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. Available from http://www.ijbs.com/v07p0992.htm