RPGeNet v2.0 allows visualizing interactions of more than 270 causative genes of inherited retinal dystrophies

RPGeNet is a network dedicated to provide a graphical platform that links retinal dystrophies causative genes with their molecular interactors. The aim of this network is granting researchers a tool that allows them to understand the pathological process in its cellular and histological context, highlight key molecular players of retinal degeneration and unveil new candidate genes of these diseases (Boloc et al., 2015).

The network uses and filters the data of BioGRID (database of biological interactions), STRING (database of protein-protein interactions) and published interactions from references in PubMed through PPaxe software (software dedicated to detecting protein interactions from scientific texts). This network was built by researchers from the University of Barcelona and includes the collaboration of Dr. Roser Gonzàlez and Dr. Gemma Marfany, founders of DBGen.

RPGeNet was designed as an interactive and easy-to-use web platform. The main page contains the search engine where the user can query the gene of interest. The search opens a new window to visualize the interaction network of the gene, at different levels and follow up interactors; it is possible to modify it at a biological level (gene expression level or recorded variants, among others) and at a graphic level (the type of graphic, the width of the lines, etc). In addition, it provides information about the source database and facilitates functions such as downloading the interactions search, loading a previous search, and downloading the image.

The second version of the software contains almost 3 times more driver genes than the previous version. In addition, it has 3,865 genes and 26,341 interactions in its skeleton; overall with 18,707 genes and 739,122 interactions in the whole network. This was achieved in part thanks to the update of the interactions in BioGRID y STRING, and additionally by the incorporation of PPaxe results. Finally, to provide better and faster management of the interaction data, RPGeNet v2.0, integrates a powerful graph-database manager engine named neo4j.

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