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

Reference#

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(info), Y11K.txt(info), Y45K.txt(info), Y78K.txt(info)

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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Kind Attachment Name Size Version Date Modified Author Change note
txt
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
pdf
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
« This particular version was published on 14-May-2011 21:38 by LingyunWu.