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
. Computational Biology and Chemistry, 30(6), 445-451, 2006.
DataSet#
The protein-protein interaction (PPI) data was obtained from MIPS (http://mips.gsf.de).
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.
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.
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, Y11K.txt
, Y45K.txt
, Y78K.txt
The resulted clusters of the four network by our analysis:
The file contains functional annotation of numerical modules.
The file contains all the matched pairs of numerical modules and experimental complexes cataloged in MIPS with logP < -16.
The file contains four modules' group which correspond to well-known biological pathways.
Figue2 shows all the pivot-like modules.
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List of attachments
Kind | Attachment Name | Size | Version | Date Modified | Author | Change note |
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20050118.txt | 600.1 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
eps |
Figure1.eps | 14.2 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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Figure2.pdf | 376.4 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
txt |
FunctionalAnnotation.txt | 163.9 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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NetMod_info.txt | 4.5 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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NetMod_links.txt | 44.4 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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NetMod_vertices.txt | 65.7 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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NetworkClusters.txt | 31.5 kB | 1 | 15-May-2011 16:40 | LingyunWu | |
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PathwayDiscovery.txt | 1.4 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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ProteinComplex.txt | 14.3 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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Y11K.txt | 143.0 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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Y2K.txt | 31.9 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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Y45K.txt | 540.0 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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Y78K.txt | 862.3 kB | 1 | 14-May-2011 21:36 | LingyunWu | |
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complexcat.scheme.txt | 72.9 kB | 1 | 14-May-2011 21:35 | LingyunWu | |
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funcat-2.0_scheme.txt | 49.4 kB | 1 | 14-May-2011 21:35 | LingyunWu |