Pathways analysis: combining microarray data and physiological data to study myogenesis

Microarray experiments investigate the changes in the expression of the transcriptome of a tissue during biological processes such as development of the tissue. Analysis usually produces a list of up and down regulated genes. While this in itself mayhighlight important biological processes taking place much information about relations between the genes may remain hidden in the huge amount of data. Databases can be searched via the internet might contain physiological information that can be invaluable for the understanding of the microarray results. However, the databases contain more information on humans and model animals such as mice and rats than other species. Therefore, we developed a set of PERL scripts enabling the automated search of the database for pathways using the list of expressed genes present on the microarray. A previously reported microarray experiment investigating prenatal myogenesis in pigs was used to search the KEGG database. Pathways returned by the KEGG database indicatedthat the gene expression patterns in several pathways suggest a single regulatory mechanism. Furthermore, pathways may be active in a specific myogenesis process such as proliferation of myoblasts or differentiation indicated by up regulated expressionof most genes in that pathway. The results also indicate that pathways act together forming networks of pathways. This may give insight in higher level regulatory mechanisms taking place in the cell. We conclude that combining microarray and physiological data such as biochemical pathways in databases accessible via the internet is an important tool for gaining biological knowledge from microarray experiments.