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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

The Figure shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray.
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Figure 8: The Figure shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray.

Mentions: A network of pathways can be constructed in two ways: (1) KEGG pathways contain boxes indicating possible connections with other pathways, and (2) genes that are active in more than one pathway may indicate direct connections between pathways interacting at the level of the biochemical path. For the latter it is enough that a single gene connects the pathways. KEGG pathway information from boxes indicating possible connections was combined with microarray data to indicate potential interaction between the pathways and used to create potential networks of pathways. For this analysis all pathways returned from the KEGG search were used. If the subpathway reaching to the box of the other pathway was found on the microarray this interaction was added to the network. Figure 8 shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray. All pathways were screened for such interactions and the networks of interactions between the pathways were created. At least two networks of pathways were found (Additional files 4). One network of pathways describes the formation and maintenance of the muscle cell cytoskeleton including a link to regulation of the contraction mechanism. The other network of pathways describes the interaction between pathways regulating the interactions between the diverse mechanisms involved in energy metabolism.


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 Figure shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: The Figure shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray.
Mentions: A network of pathways can be constructed in two ways: (1) KEGG pathways contain boxes indicating possible connections with other pathways, and (2) genes that are active in more than one pathway may indicate direct connections between pathways interacting at the level of the biochemical path. For the latter it is enough that a single gene connects the pathways. KEGG pathway information from boxes indicating possible connections was combined with microarray data to indicate potential interaction between the pathways and used to create potential networks of pathways. For this analysis all pathways returned from the KEGG search were used. If the subpathway reaching to the box of the other pathway was found on the microarray this interaction was added to the network. Figure 8 shows an example of the connection of the KEGG pathways Focal adhesion (partial pathway, Green genes) and MAPK signalling (partial pathway, blue genes). Both biochemical pathways indicate connections to each other (indicated in the boxes) and gene profiles were produced on the microarray. All pathways were screened for such interactions and the networks of interactions between the pathways were created. At least two networks of pathways were found (Additional files 4). One network of pathways describes the formation and maintenance of the muscle cell cytoskeleton including a link to regulation of the contraction mechanism. The other network of pathways describes the interaction between pathways regulating the interactions between the diverse mechanisms involved in energy metabolism.

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