Table: Interacting Pairs

The table specifies model edges, i.e. pairs of genes which interact according to the REACTOME knowledge base. The context of interaction is specified in the last column. The context can be REACTOME ID or compound from KEGG. The link is provided to REACTOME database. The first two columns specify the names of interacting genes. Input genes are presented by submitted IDs, missing genes are presented by NCBI(Entrenz) Gene Symbols.

Link to online visual output

A link to the on-line network visualization is provided here. Please note that that for online visualization you need to have Sun's Java engine installed on your machine (Version 1.5 or better). Your browser must be able to run Java applets (Turn Of Pop-up Blocker).

Link to Download network in ".xgmml" format

R spider provides you with possibility to download your model in ".xgmml" and use Cytoscape for network visualization and network editing. If the model exceeds 20 genes we strongly recommend you to use this option. You can also create high quality figures in various formats. Please, read help instructions.

Link to Download network in ".txt" format

Another option is to use Meduza program for the visualization and editing of your network. You can also create high quality figures in various formats. Please, read help instructions.

The maximal number of missing genes

Specifies the maximal allowed distance between two input genes to be considered to be connected. 0 means directly connected genes. 1 means that one intermediate gene is allowed. 2 means that two intermediate genes are allowed.

The Number of input genes (covered by the model)

Given a restriction on the maximal distance between genes, this value indicates the number of input genes in the largest connected component inferred from the input list.


The p-value indicates the probability for a random gene/protein list to have a maximal connected component of the same or larger size (accounting for the number of allowed intermediate nodes). The p-value is computed by Monte Carlo simulation. Please note that if you would submit a random gene/protein list you will get on average insignificant models.