RPGeNet v2.0

Input Genes


Here you can input a gene or multiple genes, for which you want to see as the main interactors.

You can search for any gene, but remember that this is a network built around RP/LCA causative genes and little valuable information can be found for genes outside the 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.

Gene Distance


Here you can specify how many "neighbours" your query gene(s) in the network should 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 up to what level you would like to include in your curated graph.

There are 5 levels, starting with level 0 (the skeleton - made up of all the shortest interactions between driver genes). Each additional level increases the density of the graph with more interactions and genes.

It is important to note that the higher the level, the more noise you will find.

See also tutorial page.

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 Absolute expression or three different Relative expression.

Path to


Here you can choose between trying to find the shortest pathway between your gene of interest and driver genes or to genes in the skeleton.


See also tutorial page.

  New version 2.0 of RPGeNet released. See update notes.

Network Explorer


Pathway to Level


Shortest Path between Genes