PiNGO

Finds candidate genes in a network that are associated with user-defined target GO terms.
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**For Cytoscape 3: Consider using [http://apps.cytoscape.org/apps/bingo BiNGO]** 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 : * Cytoscape graph or network file input * Limit your candidate gene search to genes already annotated to specific GO categories, or to genes not annotated to certain GO categories, or both * Customizable annotations, ontologies and reference sets, not limited to GO * Evidence code filtering * Hypergeometric or binomial test for enrichment analysis * Multiple testing correction using Bonferroni (FWER) or Benjamini&Hochberg (FDR) correction * Interactive visualization of results * extensive results in tab-delimited text file format * open source
CYTOSCAPE 2

Version 1.11

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Released 18 Jan 2011

Works with Cytoscape 2.8

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