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ClusterONEWeb

A web server implementing ClusterONE (Clustering with Overlapping Neighbourhood Expansion)

If you use this server, please consider citing at least one of these two publications:

• T. Nepusz, H. Yu, and A. Paccanaro. Detecting overlapping protein complexes in protein-protein interaction networks, Nature Methods, 9, pp. 471-472, 2012. (PubMed)
• T. Nepusz, A. E. Romero, and A. Paccanaro. ClusterONEWeb, a web server for predicting protein complexes in PPI networks, in preparation.

The source code of this server is free software released under the GPL v3.0 and can be downloaded from GitHub.

1. Upload your data file

   Select your data file on your local hard drive by clicking on the button below.

   The data file must be in a simple symbolic weighted edge list format, which looks like this:

   protein1 protein2 weight
   protein1 protein3 weight
   protein1 protein4 weight
   protein2 protein4 weight
   ...

   Protein IDs must not contain spaces. The columns must be separated by whitespace characters. Weights may be omitted; edges not having an associated weight will be considered as having unit weight.

   Click here to start uploading
2. Set the algorithm parameters

   Place the mouse over the question marks to get help on each parameter. The default parameters are recomended for a quick start.

   Basic parameters

   Minimum cluster size:  

   Minimum cluster density:  

   Advanced parameters

   Node penalty:  

   Merging method: Match coefficient Meet/min coefficient  

   Similarity function: Match coefficient Jaccard similarity Dice similarity Simpson coefficient  

   Overlap threshold:  

   Seeding method: From unused nodes From every node From every edge  

   Start the analysis
3. Examine the results

   Click on the table headers to sort the results.

   Download results Print results

   Click here to go back to the top of the table