Gene2Path: A Data Analysis Tool to Study Fish Gene Pathways by Automatic Search of Orthologous Genes

Most of the gene regulation pathways data from biochemical and molecular experiments are drawn from humans or from species commonly used as experimental animal models. Accordingly, the software packages to analyse these data on the basis of specific gene identification codes (IDs) or accession numbers (AN) are not easy to apply to other organisms that are less characterized at the genomic level. Here, we have developed the Gene2Path programme which automatically searches pathway databases to analyse microarray data in an independent, species-specific way. We have illustrated the method with data obtained from an immune targeted rainbow trout microarray to search for orthologous pathways defined for other well known biological species, such as zebrafish, although the software can be applied to any other case or species of interest. The scripts and programme are available and free at the “GENE2PATH” web site http://gene2path.no-ip.org/cgi-bin/gene2path/index.cgi. A user guide and examples are provided with the package. The Gene2Path software allows the automated searching of NCBI databases and the straightforward visualization of the data retrieved based on a graphic network environment.We thank Mario García-Lacoba for his advice and helpful comments. This work was funded by Consejo Superior de Investigaciones Cientificas (project 2010-20E084) and by Ministerio de Economia y Competitividad, (MINECO) project AGL2010- 18454 of Spain. N. Ballesteros wants to thank the MINECO for a PhD student fellowshipPeer reviewe