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Pathway Gene Swapper (PGS)

Pathway GeneSWAPPER is a Perl utility application designed to map homologous genes from one species onto the PathVisio pathway diagram of another species. Requires only a GPML PathVisio document, a CSV file of homolog mappings, and a configuration file.

Download the most recent version of the Pathway GeneSWAPPER software, source code, and documentation from our public SVN repository.

You may also download sample data files here.

Feature Description

Swap out one set of genes (or gene representations) for another in an existing PathVisio GPML file. Optionally remove literature references.

If multiple replacement genes map to a single original gene, multiple PathVisio boxes will be drawn in place of the original.

If a group associating multiple gene boxes already existed, that group will extend to any replacement genes. If no group existed previously, and multiple replacement gene boxes are required, a new group will be created.

If an original gene had multiple instances (homologs) displayed on the pathway diagram, each instance will be subjected to the replacement process. There is a "heat-map" option avaliable to help highlight homolog sets.

There is also an option to read in an extra column of gene symbols, if the user wishes to provide their own. Otherwise, the application will continue to use the label prefix and auto-numbering suffix settings.

The replacement gene symbols can be prefixed to separate them from the original, and an ordinal suffix ('-#') will be added to a group of replacement genes.

Any new gene boxes may be painted with a custom color and border, and will be stacked and offset for ease of visualization (much like a deck of cards). If the heat-map option is invoked, the custom box color will be ignored and a red-blue gradient will be applied to all mapped boxes.