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RESEARCH ARTICLE
Contents Vol 45(8)

Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data

A. Reverter A C , W. Barris A , N. Moreno-Sánchez B , S. McWilliam A , Y. H. Wang A , G. S. Harper A , S. A. Lehnert A and B. P. Dalrymple A
+ Author Affiliations
- Author Affiliations

A Cooperative Research Centre for Cattle and Beef Quality, Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia.

B Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra. de la Coruña Km. 7.5; 28040 Madrid, Spain.

C Corresponding author. Email: Tony.Reverter-Gomez@csiro.au

Australian Journal of Experimental Agriculture 45(8) 821-829 https://doi.org/10.1071/EA05039
Submitted: 14 February 2005  Accepted: 30 March 2005   Published: 26 August 2005

Abstract

We propose a data-driven reverse engineering approach to isolate the components of a gene interaction and regulatory network. We apply this method to the construction of a network for bovine skeletal muscle. Key nodes in the network include muscle-specific genes and transcription factors. muscle-specific genes are identified from data mining the USA National Cancer Institute, Cancer Genome Anatomy Project database, while transcription factors are predicted by accurate function annotation. A total of 5 microarray studies spanning 78 hybridisations and 23 different experimental conditions provided raw expression data. A recently-reported analytical method based on multivariate mixed-model equations is used to compute gene co-expression measures across 624 genes. The resulting network included 102 genes (of which 40 were muscle-specific genes and 7 were transcription factors) that clustered in 7 distinct modules with clear biological interpretation.


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