Notice: if PiNGO stalls on you while parsing annotations, try the following: a) check whether you have Java 1.6 installed, b) try running Cytoscape from cytoscape.bat (Windows) or (Linux, Mac) or modify Cytoscape’s default memory settings, see FAQ

Current version : PiNGO 1.5.1 (compatible with Cytoscape 3.4)

Notice: The current default annotations and ontologies, obtained through BiNGO, will be updated irregularly (most recent update August 2010). We encourage the use of annotation and ontology files downloaded from

If you use PiNGO in your research, please cite:

Smoot M, Ono K, Ideker T and Maere S (2011) PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics 27:1030-1.


PiNGO :  A Cytoscape plugin to find candidate genes in biological networks


PiNGO is a Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. The main advantage of PiNGO is its flexibility. PiNGO also takes full advantage of Cytoscape's versatile visualization environment.

Features include :

  1. Cytoscape graph or network file input

  2. Limit your candidate gene search to genes already annotated to specific GO categories, or to genes not annotated to certain GO categories, or both

  3. Customizable annotations, ontologies and reference sets, not limited to GO

  4. Evidence code filtering

  5. Hypergeometric or binomial test for enrichment analysis

  6. Multiple testing correction using Bonferroni (FWER) or Benjamini&Hochberg (FDR) correction

  7. Interactive visualization of results 

  8. extensive results in tab-delimited text file format

  9. open source

To get a taste, please take a look at the tutorial section.


 You may want to try our other tools too:






Copyright (c) 2010 Flanders Interuniversitary Institute for Biotechnology (VIB)