RPGeNet v1.0

About


This framework represents the retinitis pigmentosa gene interaction network, built upon 110 RP/LCA driver genes. It combines data from the iHOP, BioGRID, and STRING repositories, with additional information from GeneOntology, GeneCards, OMIM, UniProt, RefSeq, and UCSC.

Further details are available on the RPGeNet paper:
      "Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions
         to Uncover New Disease Candidates"
      Boloc et al, PLoS ONE, 2015, 10(8): e0135307.
How to use RPGeNet


Input query genes separated by commas, semicolons and/or spaces (case insensitive) in order to visualize a focused network on the query then click on "Explore Network", or choose one of the 110 RP/LCA driver genes from the dropdown list to visualize the paths that this gene shares with other RP/LCA genes and click "Get Path Genes". Here you have some examples of query genes:
       Single Genes: CERKL
       Multiple Genes: EYS, RHO, cerkl,RP1

INPUT GENES

Here you can input the retinitis pigmentosa related driver gene (RP/LCA genes), for which you want to see the main interactors.
You can search for any other gene, yet remember that this is a network built around RP/LCA causative genes and little info can be found for genes outside their scope.

You can make queries for single (i) or multiple genes (ii):
        i) Gene1
       ii) gene1,Gene2, GeNe3,...
           (case-insensitive, with or without spaces after the comma)

See also tutorial page.

NEIGHBOURHOOD GENES

Here you can specify how many "neighbours" your query gene/s in the network shoud have.
This just means that starting from your query gene/s you can just "travel" to another node with a distance equal to the value that you specified.

For example, when searching for CEP290 and the "neighbours" is set to 1 (this is the default value), this set of genes can be obtained: OFD1, RPGR, ANAPC2, ATF4, IQCB1. This means that from CEP290 one can only travel to nodes (say here genes) at distance 1. If "neighbours" is set to 2, further genes are retrieved apart from the previous ones, and now one can travel a distance of 2 to other genes.

See also tutorial page.

INTERACTION LEVEL

Here you can specify what interaction file to be used.

There are 4 interaction files describing the level of interaction: level 1, level 2, level 3 and level 4 (we choose the interaction file just by putting the number of the level, i.e 1, 2, 3 or 4). Levels above 2 may take too much to render as many nodes can be included in the drawn subnetwork.

There is also a level 0 (based on skeleton network), which represents the interactions found from network shortest paths between all pairs of RP/LCA driver genes, used as "seed" to build all the other levels.

See also tutorial page.

GENE EXPRESSION

Here you can specify how to visualize the color gradients related to gene-expression levels used to color-fill the node shapes.

You can choose between Relative and Absolute.

"Relative" gene-expression is based in the expression fold-change in retina versus the average expression on all tissues for each gene. This fold-change goes from -3 to +3, ranging from dark yellow (-3, more expressed in other tissues than in retina), white (0, no changes), to dark blue (+3, more expressed in retina than in other tissues).

"Absolute" gene-expression considers levels on retina only, and range from null expression in retina (dark yellow) to the highest expression level in retina (darkblue).

See also tutorial page.

CHOOSE A GENE

Here you can select a retinitis pigmentosa (RP) driver gene from the dropdown menu, for which you want to see the all paths connecting it with the rest of RP genes.

See also tutorial page.

INPUT GENES

Since the down of time...