Table 3

STM clustering result on the yeast PPI dataset



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

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.

Hwang et al. Algorithms for Molecular Biology 2006 1:24   doi:10.1186/1748-7188-1-24