Abstract
BackgroundCombining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet.Mammalian muscle formation has been previously studied using microarray technology in pigs because these animals are an interesting animal model for muscle formation due to selection for increased muscle mass. Results indicated regulation of the expression of genes involved in proliferation and differentiation of myoblasts, and energy metabolism. The aim of the present study was to analyse microarrays studying myogenesis in pigs. It was necessary to develop methods to search biochemical pathways databases.ResultsPERL scripts were developed that used the names of the genes on the microarray to search databases. Synonyms of gene names were added to the list by searching the Gene Ontology database. The KEGG database was searched for pathway information using this updated gene list. The KEGG database returned 88 pathways. Most genes were found in a single pathway, but others were found in up to seven pathways. Combining the pathways and the microarray information 21 pathways showed sufficient information content for further analysis. These pathways were related to regulation of several steps in myogenesis and energy metabolism. Pathways regulating myoblast proliferation and muscle fibre formation were described. Furthermore, two networks of pathways describing the formation of the myoblast cytoskeleton and regulation of the energy metabolism during myogenesis were presented.ConclusionCombining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.
Highlights
Combining microarray results and biological pathway information will add insight into biological processes
Using microarray technology we previously reported on the expression of genes known to affect myogenesis in laboratory animals and in vitro model systems [18,19,20,21]
From the 509 unique genes on the microarray with known effect on myogenesis and metabolism we found 214 unique genes with known pathway information in the Kyoto Encyclopaedia of Genes and Genomes (KEGG) database
Summary
Combining microarray results and biological pathway information will add insight into biological processes. Microarray technology can simultaneously measure the differential expression of large numbers of genes in a tissue and thereby identify the genes involved in the regulation of different stages of a process. In order to understand the biology of these data it may be relevant to include physiological information of the genes in the study Many databases such as the Kyoto Encyclopaedia of Genes and Genomes (KEGG) contain information on biological pathways [1]. Combination of microarray data and pathway data may highlight the processes taking place in the cell providing information on the tissue- and processspecific functioning of the genome. Complex genetic regulatory mechanisms underlie spatial and temporal myogenesis Central to this regulatory process is the MRF (muscle regulatory factors) gene family, four basic helix-loop-helix transcription factors regulating differentiation stage-specific gene expression [6,7]. A network of genes is involved in the regulation of the expression of the MRF genes thereby regulating the progress through the myogenesis process [8,9,10,11,12,13,14]
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