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Table 1 50 best clusters from average method with MIPS classes

From: Selection of informative clusters from hierarchical cluster tree with gene classes

Ordinal number Most enriched MIPS gene class Log-p-value Bonf. corr. log(p) Observed Clust. size Class size
1 cytoplasmic ribosomes 102.5676 99.7780 78 159 108
2 respiration chain complexes 61.0379 58.2483 28 41 31
3 mitochondrion 57.3513 54.5617 75 142 305
4 AA metabolism 55.4905 52.7009 75 259 171
5 AA biosynthesis 55.4849 52.6953 59 244 98
6 mitochondrial ribosomes 46.2851 43.4955 32 101 46
7 rRNA transcription 33.5036 30.7140 46 274 99
8 cytoplasmic ribosomes 25.8871 23.0975 15 15 108
9 nucleosomal protein complex 25.2346 22.4450 8 8 8
10 26S proteasome 23.1373 20.3477 12 21 28
11 glycolysis and gluconeogenesis 21.1692 18.3796 10 13 28
12 cytoplasmic ribosome large subunit 20.5629 17.7734 11 12 63
13 purine ribonucleotide metabolism 20.4238 17.6342 9 9 33
14 mitochondrion 19.3933 16.6038 19 24 305
15 pher. resp., mating-type determination, sex-specific proteins 18.8355 16.0460 13 15 140
16 fungal cell differentiation 18.066 15.2764 17 20 318
17 phosphate metabolism 17.3187 14.5291 9 15 29
18 lipid, FA. and isoprenoid biosynthesis 16.8961 14.1065 14 32 88
19 cytoplasmic ribosome large subunit 16.6398 13.8502 9 10 63
20 cell cycle and DNA processing 16.6338 13.8442 51 153 493
21 26S proteasome 15.6397 12.8501 8 13 28
22 aminoacyl-tRNA-synthetases 14.2599 11.4660 7 10 28
23 nucleus 13.8439 11.0544 119 475 687
24 mitochondrial ribosomes 13.1286 10.3389 7 9 46
25 carbon compound and CH. transporters 12.373 9.5834 15 235 31
26 pher. resp. 12.1225 9.3329 6 8 32
27 carbon compound and CH. utilization 12.1195 9.3299 24 114 192
28 rRNA processing 12.0528 9.2632 12 59 60
29 metabolism of energy reserves 11.7646 8.9750 11 98 30
30 nitrogen and sulfur metabolism 11.5355 8.7459 6 7 49
31 unclassified proteins 11.3345 8.5449 34 79 656
32 alpha, alpha-trehalose-phosphate synthase 11.2183 8.4287 4 10 4
33 carbon compound, CH. transport 11.0861 8.2965 15 300 30
34 splicing 11.001 8.2114 25 378 74
35 heavy metal ion transporters 10.9979 8.2083 7 34 19
36 translation 10.8811 8.0915 6 8 50
37 cation transporters 10.5607 7.7711 11 75 48
38 F0/F1 ATP synthase (complex V) 10.1474 7.3579 4 5 12
39 lipid, FA. and isoprenoid metabolism 9.8666 7.0770 7 8 159
40 cytoplasmic ribosome large subunit 9.7246 6.9350 5 5 63
41 subcellular localization 9.51 6.7204 265 562 1885
42 homeostasis of metal ions 9.5024 6.7128 10 67 50
43 AA degradation (catabolism) 8.9569 6.1673 5 12 25
44 glycine decarboxylase 8.8106 6.0210 3 5 4
45 ribonucleoside-diphosphate reductase 8.8106 6.0210 3 5 4
46 ER 8.8061 6.0165 72 1613 131
47 mitochondrial inner membrane 8.6293 5.8397 5 5 103
48 cytoskeleton 8.3735 5.5839 6 11 81
49 ER lumen 7.9589 5.1694 4 18 9
50 energy 7.3865 4.5969 5 5 181
  1. The table shows the ordinal number of the each obtained cluster shown in the figure 2, functional class that was most enriched in the cluster, and the log10-p-value for the most enriched class with and without Bonferroni-correction. Table shows also number of class members in the cluster (observed), size of the cluster (clust. size), and size of the functional class. The five most enriched functional classes can be found from table 4 [additional file 1]. Notice clusters that include only or almost only functional class members (8, 9, 12, 13, 15, 19 etc.) and the clusters that include the whole or almost the whole functional class (2, 9, 32 etc.). An especially good example is cluster 9 as it includes all the histone complex members and only histone complex members. Also it is worthwhile to notice the extremely small obtained p-values (for example, log-p-value 12 would refer to p-value 10-12). Abbreviations are: AA, amino acid; metab, metabolism; pher. resp. pheromone response; CH, carbohydrate; FA, fatty-acid. More details of these results are shown in table 4 [Additional file: 1].