__PPICPM__: Identification of functional modules in PPI network by clique percolation clustering


!!!Reference

* Shihua Zhang, Xue-Mei Ning and Xiang-Sun Zhang. __[Identification of functional modules in a PPI network by clique percolation clustering|http://linkinghub.elsevier.com/retrieve/pii/S1476927106000867]__. ''Computational Biology and Chemistry'', 30(6), 445-451, 2006.


!!!DataSet

The protein-protein interaction (PPI) data was obtained from MIPS ([http://mips.gsf.de]). 
* [PPI_data.txt|File:PPICPM/20050118.txt]

They are functional classification catalogue scheme (Version 2.0, 18.03.2004) and protein complexes catalogue scheme (23.03.2005) respectively. So the detailed information of functional annotation and matched complexes of numerically computed modules can be seen.
* [funcat-2.0_scheme|File:PPICPM/funcat-2.0_scheme.txt]
* [complexcat.scheme|File:PPICPM/complexcat.scheme.txt]


!!!Results


These files include modules' member, modules' links, and modules' information such as sizes of modules, number of modules' links and its cc-value respectively.
* [NetMod_vertices.txt|File:PPICPM/NetMod_vertices.txt]
* [NetMod_links.txt|File:PPICPM/NetMod_links.txt]
* [NetMod_info.txt|File:PPICPM/NetMod_info.txt]


!!!Comparison with RNSC

Table 1 Results of two network clustering method under the same condition.
|| Network || Minimum size || RNSC clusters || Our clusters
| Y2k  | 4 | 48 | 57
| Y11k | 5 | 84 | 76
| Y45k | 7 | 86 | 119
| Y78k | 8 | 90 | 128

Four networks: [Y2K.txt|File:PPICPM/Y2K.txt], [Y11K.txt|File:PPICPM/Y11K.txt], [Y45K.txt|File:PPICPM/Y45K.txt], [Y78K.txt|File:PPICPM/Y78K.txt]

The resulted clusters of the four network by our analysis:
* [NetworkClusters.txt|File:PPICPM/NetworkClusters.txt]

The file contains functional annotation of numerical modules.
* [FunctionalAnnotation.txt|File:PPICPM/FunctionalAnnotation.txt]

The file contains all the matched pairs of numerical modules and experimental complexes cataloged in MIPS with logP < -16.
* [ProteinComplex.txt|File:PPICPM/ProteinComplex.txt]

The file contains four modules' group which correspond to well-known biological pathways.
* [PathwayDiscovery.txt|File:PPICPM/PathwayDiscovery.txt]

Figue2 shows all the pivot-like modules.
* [Figure2.pdf|File:PPICPM/Figure2.pdf]


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