title: A gene coexpression network for bovine skeletal muscle inferred from microarray data.
abstract: We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and we explore 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism, and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP, and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins or of titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast-twitch muscle structural proteins and enzymes was observed, but slow-twitch-specific proteins were not correlated with the fast-twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.
authors.affiliation: Bioinformatics Group, Commonwealth Scientific and Industrial Research Organisation Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia. Tony.Reverter-Gomez@csiro.au
authors.forename: Antonio
authors.initials: A
authors.lastname: Reverter
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Hudson
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.forename: Siok-Hwee
authors.initials: SH
authors.lastname: Tan
authors.forename: Wes
authors.initials: W
authors.lastname: Barris
authors.forename: Keren A
authors.initials: KA
authors.lastname: Byrne
authors.forename: Sean M
authors.initials: SM
authors.lastname: McWilliam
authors.forename: Cynthia D K
authors.initials: CD
authors.lastname: Bottema
authors.forename: Adam
authors.initials: A
authors.lastname: Kister
authors.forename: Paul L
authors.initials: PL
authors.lastname: Greenwood
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Harper
authors.forename: Sigrid A
authors.initials: SA
authors.lastname: Lehnert
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism; D000818:Animals; D002417:Cattle; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008274:Magnesium / Q000378:metabolism; D008954:Models, Biological; D018482:Muscle, Skeletal / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D014176:Protein Biosynthesis; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D014157:Transcription Factors; D008274:Magnesium