title: Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs.
abstract: BACKGROUND
  Combining 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.
  
  
  RESULTS
  PERL 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.
  
  
  CONCLUSIONS
  Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.
authors.affiliation: Animal Breeding and Genetics Centre, Animal Sciences Group, Wageningen University and Research Centre, Lelystad, The Netherlands. marinus.tepas@wur.nl
authors.forename: Marinus F W
authors.initials: MF
authors.lastname: Te Pas
authors.forename: Ina
authors.initials: I
authors.lastname: Hulsegge
authors.forename: Albart
authors.initials: A
authors.lastname: Coster
authors.forename: Marco H
authors.initials: MH
authors.lastname: Pool
authors.forename: Henri H
authors.initials: HH
authors.lastname: Heuven
authors.forename: Luc L G
authors.initials: LL
authors.lastname: Janss
mesh_terms: D000818:Animals; D002118:Calcium / Q000378:metabolism; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D005865:Gestational Age; D053858:Metabolic Networks and Pathways / Q000502:physiology*; D024510:Muscle Development / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D011247:Pregnancy; D051880:Receptors, Notch / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology; D013552:Swine; D051153:Wnt Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D051880:Receptors, Notch; D051153:Wnt Proteins; D002118:Calcium