Limits...
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.

Show MeSH

Related in: MedlinePlus

The WNT signalling KEGG pathway consisting of three subpathways with the genes on the microarray encircled (A) and expression profiles of genes during porcine myogenesis (B). The expression profiles indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. All genes on the microarray are located on the top subpathway directed to influence the cell cycle, i.e. proliferation of myoblasts in myogenesis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1919358&req=5

Figure 5: The WNT signalling KEGG pathway consisting of three subpathways with the genes on the microarray encircled (A) and expression profiles of genes during porcine myogenesis (B). The expression profiles indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. All genes on the microarray are located on the top subpathway directed to influence the cell cycle, i.e. proliferation of myoblasts in myogenesis.

Mentions: The Notch family of receptors is activated by their ligands, the Delta gene family, activating a pathway leading to up regulation of myf-5 and down regulation of MyoD expression resulting in blocking of differentiation. As a result the myoblasts are kept in an undifferentiated proliferative state [22,23]. Figure 4 shows the Notch signalling pathway derived from the KEGG database with the genes on the microarray encircled (Figure 4A) and their corresponding expression profiles (Figure 4B). The expression profiles in Figures 4, 5, 6, 7 indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. Since all genes are located in a single biochemical pathway there are no subpathways. The profile indicates that expression is increased during development twice related to age, and subsequent to developmental stage of myogenesis. The timing of the increases suggests that the expression profile is related to the primary and secondary waves of myofibre formation in pigs. Furthermore, since most genes do show similar expression profiles this may indicate regulation of the expression of all genes in the pathway by a single mechanism. The profiles and regulatory mechanism may indicate a major function of the Notch pathway in porcine myogenesis.


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)

The WNT signalling KEGG pathway consisting of three subpathways with the genes on the microarray encircled (A) and expression profiles of genes during porcine myogenesis (B). The expression profiles indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. All genes on the microarray are located on the top subpathway directed to influence the cell cycle, i.e. proliferation of myoblasts in myogenesis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: The WNT signalling KEGG pathway consisting of three subpathways with the genes on the microarray encircled (A) and expression profiles of genes during porcine myogenesis (B). The expression profiles indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. All genes on the microarray are located on the top subpathway directed to influence the cell cycle, i.e. proliferation of myoblasts in myogenesis.
Mentions: The Notch family of receptors is activated by their ligands, the Delta gene family, activating a pathway leading to up regulation of myf-5 and down regulation of MyoD expression resulting in blocking of differentiation. As a result the myoblasts are kept in an undifferentiated proliferative state [22,23]. Figure 4 shows the Notch signalling pathway derived from the KEGG database with the genes on the microarray encircled (Figure 4A) and their corresponding expression profiles (Figure 4B). The expression profiles in Figures 4, 5, 6, 7 indicate the gestational age at the X-axis and the expression profile as indicated by the differential expression on the microarray on the Y-axis. Since all genes are located in a single biochemical pathway there are no subpathways. The profile indicates that expression is increased during development twice related to age, and subsequent to developmental stage of myogenesis. The timing of the increases suggests that the expression profile is related to the primary and secondary waves of myofibre formation in pigs. Furthermore, since most genes do show similar expression profiles this may indicate regulation of the expression of all genes in the pathway by a single mechanism. The profiles and regulatory mechanism may indicate a major function of the Notch pathway in porcine myogenesis.

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