PCP
Version 1.0
==============
 

There are two programs:

 

1)       filter_int 

This is a perl program that pre-processes the input interaction network.

 

usage: filter_int -i interactions [-w fsweight_threshold] [-l] [-o output_file]

E.g. filter_int -i interactions.txt -w 0.4 -l -o new_interactions.txt

 

options:

 

-i :    Interaction file (tab delimited text file with 3 columns: 
                          Protein_A, Protein_B and fs-weight score)

-l :    Include Indirect Interactions

-w :    FS-Weight threshold for filtering interactions (default = 0.2), we used 0.4.
            For more info on FS-weight, see Refs 2 and 3.

-o :    Output interaction file (default = output.txt). 
        The output file will be in the same format as the input interaction file.

 

 

2)       pcp 

This is a C++ implementation of the PCP algorithm.

 

usage: pcp interaction_file ICD_threshold min clique size

E.g. pcp interactions.txt 0.1 2

 

The interaction file is the output file from filter_int.

ICD_threshold is the threshold for which iterative partial clique 
        merging terminates (we use 0.1)

Min Clique size is the min size of cliques to be used from the 
       clique finding step (we use 2)

 
Also included are the two interactions files and the two MIPS complex datasets 
used in the PCP paper [ref 1].


Credits:

These two programs are implemented by CHUA Hon Nian and NING Kang. 
The project is supported in part by an NGS scholarship, and 
URC grant "R-252-000-274-112: Graph-Based Protein Function Prediction". 
If you use this program, please cite Refs 1, 2, 3, 4 below.


References:

[1]     Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong. (2007) 
        Using Indirect Protein-Protein Interactions for Protein Complex Prediction. 
        Proceedings of 6th Annual International Conference on Computational 
        Systems Bioinformatics (CSB2007), San Diego, California, August 2007.

[2]	H. N. Chua, W.K. Sung, L. Wong. (2006)
	Exploiting indirect neighbours and topological weight to predict 
	protein function from protein-protein interactions. 
	Bioinformatics, 22:1623-1630.
	
[3]	H. N. Chua, W.K. Sung, L. Wong. (2007)
	Using Indirect Protein Interactions for the Prediction of Gene 
	Ontology Functions. 
	BMC Bioinformatics, 8(Suppl 4):S8.

[4]     Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong. 
        Using Indirect Protein-Protein Interactions for Protein Complex Prediction. 
        Journal of Bioinformatics and Computational Biology, 6(3):435--466, June 2008.