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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 workflow diagram describing the individual steps taken by the software from microarray data to physiological understanding via pathways analysis. Step 1: A PERL script uses a text file with a list of all genes on the microarray to search the Gene Ontology database for synonyms. These Synonyms are added to the gene list. Step 2 uses this updated gene list to search the KEGG pathway database for pathways in which the genes are involved. If one or more pathways were found for a gene the KEGG database returns a list of pathway names for that gene and a link to the reference pathway for each pathway. Both are added to the file. Step 3 combines the results of the microarray and the pathways. All genes of the pathway represented on the microarray have an expression pattern consisting of the expression in the Longissimus muscle at seven time points during gestation. First all genes of the pathway are considered. Secondly, if more than one biochemical path is specified by the pathway (i.e. called subpathways) the individual subpathways are investigated separately. Thirdly, if KEGG-pathways are linked either because the pathway indicates it or because at least one gene is found in two or more pathways, a network of these pathways is constructed. In step 4 the expression patterns of these pathways and networks were analysed for comparable expression patterns that may indicate common regulatory events linking genes in pathways, subpathways, or networks of pathways creating biological understanding of the physiology of the studied processes.
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Figure 1: The workflow diagram describing the individual steps taken by the software from microarray data to physiological understanding via pathways analysis. Step 1: A PERL script uses a text file with a list of all genes on the microarray to search the Gene Ontology database for synonyms. These Synonyms are added to the gene list. Step 2 uses this updated gene list to search the KEGG pathway database for pathways in which the genes are involved. If one or more pathways were found for a gene the KEGG database returns a list of pathway names for that gene and a link to the reference pathway for each pathway. Both are added to the file. Step 3 combines the results of the microarray and the pathways. All genes of the pathway represented on the microarray have an expression pattern consisting of the expression in the Longissimus muscle at seven time points during gestation. First all genes of the pathway are considered. Secondly, if more than one biochemical path is specified by the pathway (i.e. called subpathways) the individual subpathways are investigated separately. Thirdly, if KEGG-pathways are linked either because the pathway indicates it or because at least one gene is found in two or more pathways, a network of these pathways is constructed. In step 4 the expression patterns of these pathways and networks were analysed for comparable expression patterns that may indicate common regulatory events linking genes in pathways, subpathways, or networks of pathways creating biological understanding of the physiology of the studied processes.

Mentions: The list of gene names on the microarray was used to identify pathways in which the genes could be active in the cell (see workflow diagram, Figure 1). The first PERL script collected all synonyms of genes on the array at the GO database. A total of 1524 synonyms of the 509 genes on the microarray were found and added to the list, ranging from zero to a maximum of 56 synonyms in one extreme case (the RPS3 gene). However, it should be noted that not all of these so called synonyms were usable in the pathway database search. Of these 1524 synonyms 22 were contig numbers, 81 were ORF (open reading frame) numbers, and 30 were chromosome localisation numbers. The updated list was used by the second PERL script to search the KEGG database for pathways. 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 KEGG database. These 214 genes were shown to be active in a total of 88 pathways. The number of genes with microarray information differed per pathway. Figure 2 shows that the number of genes on the microarray differed per pathway. While 37 pathways were represented with only a single gene on the microarray the maximum number of genes on the microarray per pathway was 28. Microarray data from a single gene of a pathway is not sufficient to describe a common regulatory mechanism of a pathway. Furthermore, microarray information of two genes of a pathway not related to a biochemical path is similarly not sufficient to describe a common regulatory mechanism. Therefore, pathways with at least two genes with information on the microarray and localized on one biochemical path were further analysed. Due to this several of these pathways were called not conclusive because of 1 gene entry with microarray data) or low informative (two or more gene entries, but not in a single biochemical path) (Table 1). Twenty-one pathways were further analysed. From the genes on these pathways 5–32 percent was represented on 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)

The workflow diagram describing the individual steps taken by the software from microarray data to physiological understanding via pathways analysis. Step 1: A PERL script uses a text file with a list of all genes on the microarray to search the Gene Ontology database for synonyms. These Synonyms are added to the gene list. Step 2 uses this updated gene list to search the KEGG pathway database for pathways in which the genes are involved. If one or more pathways were found for a gene the KEGG database returns a list of pathway names for that gene and a link to the reference pathway for each pathway. Both are added to the file. Step 3 combines the results of the microarray and the pathways. All genes of the pathway represented on the microarray have an expression pattern consisting of the expression in the Longissimus muscle at seven time points during gestation. First all genes of the pathway are considered. Secondly, if more than one biochemical path is specified by the pathway (i.e. called subpathways) the individual subpathways are investigated separately. Thirdly, if KEGG-pathways are linked either because the pathway indicates it or because at least one gene is found in two or more pathways, a network of these pathways is constructed. In step 4 the expression patterns of these pathways and networks were analysed for comparable expression patterns that may indicate common regulatory events linking genes in pathways, subpathways, or networks of pathways creating biological understanding of the physiology of the studied processes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The workflow diagram describing the individual steps taken by the software from microarray data to physiological understanding via pathways analysis. Step 1: A PERL script uses a text file with a list of all genes on the microarray to search the Gene Ontology database for synonyms. These Synonyms are added to the gene list. Step 2 uses this updated gene list to search the KEGG pathway database for pathways in which the genes are involved. If one or more pathways were found for a gene the KEGG database returns a list of pathway names for that gene and a link to the reference pathway for each pathway. Both are added to the file. Step 3 combines the results of the microarray and the pathways. All genes of the pathway represented on the microarray have an expression pattern consisting of the expression in the Longissimus muscle at seven time points during gestation. First all genes of the pathway are considered. Secondly, if more than one biochemical path is specified by the pathway (i.e. called subpathways) the individual subpathways are investigated separately. Thirdly, if KEGG-pathways are linked either because the pathway indicates it or because at least one gene is found in two or more pathways, a network of these pathways is constructed. In step 4 the expression patterns of these pathways and networks were analysed for comparable expression patterns that may indicate common regulatory events linking genes in pathways, subpathways, or networks of pathways creating biological understanding of the physiology of the studied processes.
Mentions: The list of gene names on the microarray was used to identify pathways in which the genes could be active in the cell (see workflow diagram, Figure 1). The first PERL script collected all synonyms of genes on the array at the GO database. A total of 1524 synonyms of the 509 genes on the microarray were found and added to the list, ranging from zero to a maximum of 56 synonyms in one extreme case (the RPS3 gene). However, it should be noted that not all of these so called synonyms were usable in the pathway database search. Of these 1524 synonyms 22 were contig numbers, 81 were ORF (open reading frame) numbers, and 30 were chromosome localisation numbers. The updated list was used by the second PERL script to search the KEGG database for pathways. 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 KEGG database. These 214 genes were shown to be active in a total of 88 pathways. The number of genes with microarray information differed per pathway. Figure 2 shows that the number of genes on the microarray differed per pathway. While 37 pathways were represented with only a single gene on the microarray the maximum number of genes on the microarray per pathway was 28. Microarray data from a single gene of a pathway is not sufficient to describe a common regulatory mechanism of a pathway. Furthermore, microarray information of two genes of a pathway not related to a biochemical path is similarly not sufficient to describe a common regulatory mechanism. Therefore, pathways with at least two genes with information on the microarray and localized on one biochemical path were further analysed. Due to this several of these pathways were called not conclusive because of 1 gene entry with microarray data) or low informative (two or more gene entries, but not in a single biochemical path) (Table 1). Twenty-one pathways were further analysed. From the genes on these pathways 5–32 percent was represented on 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