About

Retinitis pigmentosa is a highly heterogenous disease with now over 200 known driver genes. With such high hetergeneity, RPGeNet, a web application tool, was created to help users find new potential driver genes of retinitis pigmentosa and help better visualize the complex interaction network of the retina. The interaction database is formed by the merger of self-curated BioGRID, STRING and text-mining (PPaxe) interaction data. The database is managed by neo4j, the graph's visual display is created by Cytoscape.js, and the web interface is implemented on a django framework.

Currently, RPGeNet counts with 276 driver genes, 18,542 total nodes (genes/proteins), and 1,218,032 total directed edges (interactions, defining 613,319 non-redundant edges), derived from 3,209,871 total evidences gathered from the three aforementioned sources. Further information is available on our data page and our published paper.

RPGeNet was created by Compgen Lab and Marfany Laboratory at the University of Barcelona.

Citing RPGeNet

RPGeNet v2.0: expanding the universe of retinal disease gene interactions network.
R. Arenas-Galnares, S. Castillo-Lara, V. Toulis, D. Boloc, R. Gonzàlez-Duarte, G. Marfany, J.F. Abril.
Database, 2019, baz120. OPEN ACCESS

Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates.
Daniel Boloc, Sergio Castillo-Lara, Gemma Marfany, Roser Gonzàlez-Duarte and Josep F. Abril.
PLoS ONE, 2015, 10(8): e0135307. OPEN ACCESS

Link to Previous Versions

RPGeNet v1.0

Update Notes

September 5th, 2019 - Version 2.0.2

Improved interaction information cards, the new layout now displays further details about the suppporting evidences on each interaction and provides more links to external references.
Fixed a bug where some synonim identifiers were mapped as standard symbols, which duplicated some nodes in the core network.
RPGeNet now has 4,018 genes and 35,528 interactions in its skeleton; with 18,542 genes and 1,218,032 interactions in the network overall.

April 29th, 2019 - Version 2.0.1

BioGRID data was updated to version 3.5.171
STRING data was updated to version 11.0
RPGeNet now has 4,086 genes and 34,077 interactions in its skeleton; with 19,416 genes and 1,210,705 interactions in the network overall.

October 20th, 2018 - Version 2.0

The number of driver genes has increased to 276 from the original 75 genes
RPGeNet has revised its network with updated interactions from BioGRID and STRING but also new interactions text-mined using PPaxe.
RPGeNet now has 3,865 genes and 26,341 interactions in its skeleton; with 18,707 genes and 739,122 interactions in the network overall.
A new graph-base database manager, neo4j, has been implemented.