HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: 28/1/76    most recent 00105.2006v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Web of Science (1) Citing Articles via Google Scholar Google Scholar Articles by Reverter, A. Articles by Dalrymple, B. P. Search for Related Content PubMed PubMed Citation Articles by Reverter, A. Articles by Dalrymple, B. P.

Call For Papers: 2nd International Symposium on Animal Functional Genomics

A gene coexpression network for bovine skeletal muscle inferred from microarray data

Cooperative Research Centre for Cattle and Beef Quality
¹ Commonwealth Scientific and Industrial Research Organisation (CSIRO) Livestock Industries, St. Lucia, Queensland
² Agriculture and Animal Science, University of Adelaide, Roseworthy, South Australia
³ New South Wales Department of Primary Industries, University of New England, Armidale, New South Wales, Australia

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.

This article has been cited by other articles:

				A. Reverter and E. K. F. Chan Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks Bioinformatics, November 1, 2008; 24(21): 2491 - 2497. [Abstract] [Full Text] [PDF]

				Y. Noguchi, N. Shikata, Y. Furuhata, T. Kimura, and M. Takahashi Characterization of dietary protein-dependent amino acid metabolism by linking free amino acids with transcriptional profiles through analysis of correlation Physiol Genomics, August 1, 2008; 34(3): 315 - 326. [Abstract] [Full Text] [PDF]

				J. L. Burton and G. J. M. Rosa Physiological genomics special issue on animal functional genomics Physiol Genomics, December 13, 2006; 28(1): 1 - 4. [Full Text] [PDF]