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Table 3 STM clustering result on the yeast PPI dataset

From: A novel functional module detection algorithm for protein-protein interaction networks

    Distribution   
Cluster Size Density H D U -Logp Function
1 214 0.019 24.7 69.6 5.6 43.9 Nuclear transport
2 188 0.015 69.1 25.0 5.8 36.4 Cell cycle and DNA processing
3 181 0.022 22.0 72.3 5.5 17.2 Cytoplasmic and nuclear protein degradation
4 170 0.028 46.4 42.9 10.5 31.6 Transported compounds (substrates)
5 131 0.028 37.4 55.7 6.8 28.6 Vesicular transport (Golgi network, etc.)
6 125 0.030 60.8 33.6 5.6 32.2 tRNA synthesis
7 113 0.027 19.4 71.6 8.8 11.8 Actin cytoskeleton
8 79 0.045 17.7 73.4 8.8 12.3 Homeostasis of protons
9 78 0.033 26.9 62.8 10.2 12.5 Ribosome biogenesis
10 76 0.041 38.1 59.2 2.6 20.2 rRNA processing
11 72 0.030 5.6 84.7 9.7 6.2 Calcium binding
12 68 0.064 66.1 25.0 8.8 44.5 mRNA processing
13 61 0.041 40.9 52.4 6.5 11.5 Cytoskeleton
14 58 0.064 72.4 27.6 0.0 37.4 General transcription activities
15 53 0.048 15.0 71.6 13.2 7.9 MAPKKK cascade
16 50 0.064 66.0 32.0 2.0 33.5 rRNA processing
17 45 0.055 24.4 73.3 2.2 11.1 Metabolism of energy reserves
18 44 0.058 59.0 36.3 4.5 5.1 Metabolism
19 39 0.072 10.2 89.7 0.0 7.3 Cell-cell adhesion
20 36 0.125 58.3 36.1 5.5 16.9 Vesicular transport
21 29 0.091 55.1 44.8 0.0 8.3 Phosphate metabolism
22 28 0.074 14.2 78.5 7.1 4.5 Lysosomal and vacuolar protein degradation
23 27 0.119 29.6 66.6 3.7 7.3 Cytokinesis (cell division)/septum formation
24 26 0.153 53.8 46.1 0.0 28.6 Peroxisomal transport
25 25 0.090 28.0 68.0 4.0 4.6 Regulation of C-compound and carbohydrate utilization
26 25 0.116 68.0 28 4.0 12.9 Cell fate
27 22 0.151 59.0 36.3 4.5 11.4 DNA conformation modification
28 21 0.147 76.1 19.0 4.7 23.9 Mitochondrial transport
29 20 0.200 75.0 20.0 5.0 24.0 rRNA synthesis
30 19 0.228 78.9 15.7 5.2 17.9 Splicing
31 17 0.220 70.5 29.4 0.0 19.7 Microtubule cytoskeleton
32 17 0.183 23.5 76.4 0.0 8.2 Regulation of nitrogen utilization
33 15 0.304 86.6 13.3 0.0 31.3 Energy generation
34 14 0.142 50.0 42.8 7.1 9.0 Small GTPase mediated signal transduction
35 13 0.564 76.9 23.0 0.0 15.9 Mitosis
36 13 0.358 84.6 15.4 0.0 12.4 DNA conformation modification
37 13 0.410 69.2 23.0 7.6 17.6 3'-end processing
38 13 0.179 61.5 30.7 7.6 6.7 DNA recombination and DNA repair
39 12 0.196 16.6 75.0 8.3 3.9 Unspecified signal transduction
40 12 0.363 58.3 41.6 0.0 14.7 Posttranslational modification of amino acids
41 12 0.166 16.6 75.0 8.3 2.4 Autoproteolytic processing
42 11 0.218 54.5 45.4 0.0 2.9 Transcriptional control
43 11 0.200 72.7 27.2 0.0 8.2 Enzymatic activity regulation/enzyme regulator
44 10 0.466 80.0 20.0 0.0 14.8 Translation initiation
45 9 0.361 77.7 22.2 0.0 12.8 Translation initiation
46 8 0.321 50.0 37.5 12.5 5.6 Metabolism of energy reserves
47 8 0.321 75.0 25.0 0.0 9.0 Modification by ubiquitination, deubiquitination
48 8 0.321 37.5 62.5 0.0 3.7 Mitosis
49 7 0.333 42.8 57.1 0.0 3.5 DNA damage response
50 7 0.333 57.1 28.5 14.2 4.1 Vacuolar transport
51 7 0.285 28.5 71.4 0.0 4.4 Biosynthesis of serine
52 6 0.333 50.0 33.3 16.6 2.38 Modification by phosphorylation, dephosphorylation, etc.
53 5 0.400 100 0.0 0.0 7.0 Meiosis
54 5 0.600 100 0.0 0.0 7.0 Vacuolar transport
55 5 0.400 100 0.0 0.0 8.5 ER to Golgi transport
56 5 0.400 20.0 40.0 40.0 1.8 cAMP mediated signal transduction
57 5 0.500 40.0 40.0 20.0 3.1 Oxidative stress response
58 5 0.500 80.0 20.0 0.0 4.4 Intracellular signalling
59 5 0.600 40.0 60.0 0.0 4.2 Tetracyclic and pentacyclic triterpenes
60 5 0.400 60.0 40.0 0.0 4.1 Mitochondrial transport
  1. The first column is a cluster identifier; the Size column indicates the number of proteins in each cluster; the Density indicates the density of the cluster; the H column indicates the percentage of proteins concordant with the major function indicated in the last column; the D column indicates the percentage of proteins discordant with the major function and U column indicates percentage of proteins not assigned to any function.