PRINCIPLE: PRINCE Plugin

PRINCE (PRIoritizatioN and Complex Elucidation) is a method for prioritizing disease associated genes.
PRINCIPLE (PRINCe ImPLEmentation) is a client-server implementation of PRINCE, where the client side is implemented as a plugin in Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization

Citing

Please cite the following papers:
  1. PRINCIPLE: A tool for associating genes with diseases via network propagation,Gottlieb A., Magger O., Berman I., Ruppin E. and Sharan R. Bioinformatics 2011 ;doi: 10.1093/bioinformatics/btr584
  2. Associating genes and protein complexes with disease via network propagation,Vanunu, O., Magger, O., Ruppin, E., Shlomi, T. and Sharan, R. PLoS Comput Biol, 2010, 6, e1000641.

Prerequisites

  1. Internet connection: PRINCIPLE plugin connects to the PRINCIPLE server, where computations are performed
  2. Java Runtime environment (JRE). Download JRE version 6 or higher. Pay attention that the plugin does not work with java 1.5.
  3. Cytoscape version 2.7.0 or newer

Mac OS users may find following links useful:

  1. Apple's official java 6 for Mac 10.5 (64-bit Intel-based Macs only)
    1. Updating your java version to 1.6 .
    2. Switching you default java version
  2. SoyLatte java 6 for Mac 10.4 or 10.5 (Intel)
    1. Install SoyLatte
    2. Add the following to your path (or to the cytoscape.sh file):
      1. open /Applications/Utilities/X11.app
      2. export PATH=<bin directory of SoyLatte>:$PATH
      3. export DISPLAY=:0.0

Downloads

You can download the zipped similarity file (PhenSim.zip) and unzip on your local computer or alternatively download the raw file (PhenSim.tsv)


File Date Size Download Comments
User Guide 2011-09-21 945KB UserGuide.pdf User Guide
PRINCIPLE plugin (v1.0) 2011-09-23 224KB PrincePlugin.jar
Phenotypic disease similarity 2011-08-14 183MB PhenSim.tsv Disease-disease phenotypic similarity, based on
van Driel et al. (2006) A text-mining analysis of the human phenome. Eur J Hum Genet 14: 535-542
Phenotypic disease similarity (zipped) 2011-09-15 69MB PhenSim.zip Disease-disease phenotypic similarity, based on
van Driel et al. (2006) A text-mining analysis of the human phenome. Eur J Hum Genet 14: 535-542
Diseases 2011-08-14 227KB phenotype.xref The ordered list of diseases (MIM code and disease name)
OMIM disease-gene associations 2011-08-14 24KB associations.txt Associations between diseases and genes

Contact

In case of problems, please send an e-mail to principle.help AT gmail.com

Last updated: 2011-08-14