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Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs.

Te Pas MF, Hulsegge I, Coster A, Pool MH, Heuven HH, Janss LL - BMC Dev. Biol. (2007)

Bottom Line: Combining microarray results and biological pathway information will add insight into biological processes.Most genes were found in a single pathway, but others were found in up to seven pathways.Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genetics Centre, Animal Sciences Group, Wageningen University and Research Centre, Lelystad, The Netherlands. marinus.tepas@wur.nl

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.

Conclusion: Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.

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Related in: MedlinePlus

Number of pathways per gene. The KEGG database was screened for pathway information of genes on the microarray with known effect on myogenesis. While most genes were found active in a single pathway, many others proved to be involved in more than one pathway with a maximum of seven pathways for a single gene
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Figure 3: Number of pathways per gene. The KEGG database was screened for pathway information of genes on the microarray with known effect on myogenesis. While most genes were found active in a single pathway, many others proved to be involved in more than one pathway with a maximum of seven pathways for a single gene

Mentions: We also observed that genes could be active in more than one pathway. Figure 3 show that 160 of the 214 unique genes the KEGG database reported information on one pathway, while one gene was found in seven different pathways. In total we observed information of more than one pathway per gene for 54 genes. This may be a result of the network of pathways that together constitute the processes inside the living cell, but those genes were not covered by the microarray.


Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs.

Te Pas MF, Hulsegge I, Coster A, Pool MH, Heuven HH, Janss LL - BMC Dev. Biol. (2007)

Number of pathways per gene. The KEGG database was screened for pathway information of genes on the microarray with known effect on myogenesis. While most genes were found active in a single pathway, many others proved to be involved in more than one pathway with a maximum of seven pathways for a single gene
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1919358&req=5

Figure 3: Number of pathways per gene. The KEGG database was screened for pathway information of genes on the microarray with known effect on myogenesis. While most genes were found active in a single pathway, many others proved to be involved in more than one pathway with a maximum of seven pathways for a single gene
Mentions: We also observed that genes could be active in more than one pathway. Figure 3 show that 160 of the 214 unique genes the KEGG database reported information on one pathway, while one gene was found in seven different pathways. In total we observed information of more than one pathway per gene for 54 genes. This may be a result of the network of pathways that together constitute the processes inside the living cell, but those genes were not covered by the microarray.

Bottom Line: Combining microarray results and biological pathway information will add insight into biological processes.Most genes were found in a single pathway, but others were found in up to seven pathways.Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.

View Article: PubMed Central - HTML - PubMed

Affiliation: Animal Breeding and Genetics Centre, Animal Sciences Group, Wageningen University and Research Centre, Lelystad, The Netherlands. marinus.tepas@wur.nl

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.

Conclusion: Combining microarray results and pathways information available through the internet provide biological insight in how the process of porcine myogenesis is regulated.

Show MeSH
Related in: MedlinePlus