Table 2.
Distribution of genes belonging to specific functional categories among the six hierarchical clusters
| Main category according to FunCat or (4) | FunCat sub categorya or table number | Observed or expectedb | Max0 | Max0.5 | Max1 | Max1∼4 | Max8∼16 | Min0∼0.5 | Other | Totalc | P-valued |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Biogenesis of cellular components | Obs | 0 | 4 | 6 | 5 | 1 | 7 | 1 | 24 | 0.914 | |
| Exp | 2.6 | 3.4 | 4.3 | 2.6 | 1.7 | 8.6 | 0.9 | ||||
| Cell cycle and DNA processing | Obs | 0 | 16 | 16 | 17 | 1 | 16 | 6 | 72 | 0.013 | |
| Exp | 7.7 | 10.3 | 12.9 | 7.7 | 5.1 | 25.7 | 2.6 | ||||
| Cell cycle and DNA processing | DNA processing (2nd) | Obs | 0 | 7 | 4 | 8 | 0 | 4 | 2 | 25 | 0.039 |
| Exp | 0.5 | 2.7 | 6.1 | 4.2 | 1.7 | 7.2 | 2.6 | ||||
| Cell fate | Obs | 3 | 6 | 11 | 7 | 1 | 15 | 4 | 47 | 0.403 | |
| Exp | 5.0 | 6.7 | 8.4 | 5.0 | 3.4 | 16.8 | 1.7 | ||||
| Cell rescue, defense and virulence | Obs | 2 | 8 | 12 | 6 | 7 | 18 | 4 | 57 | 0.307 | |
| Exp | 6.1 | 8.1 | 10.2 | 6.1 | 4.1 | 20.4 | 2.0 | ||||
| Cell type differentiation | Obs | 3 | 8 | 10 | 6 | 2 | 12 | 3 | 44 | 0.247 | |
| Exp | 4.7 | 6.3 | 7.9 | 4.7 | 3.1 | 15.7 | 1.6 | ||||
| Cellular communication/signal transduction mechanism | Obs | 0 | 1 | 13 | 6 | 2 | 22 | 4 | 48 | 0.128 | |
| Exp | 5.1 | 6.9 | 8.6 | 5.1 | 3.4 | 17.1 | 1.7 | ||||
| Cellular transport, transport facilities and transport routes | Obs | 0 | 7 | 22 | 23 | 11 | 44 | 4 | 111 | 0.003 | |
| Exp | 11.9 | 15.9 | 19.8 | 11.9 | 7.9 | 39.6 | 4.0 | ||||
| Cellular transport, transport facilities and transport routes | Transport facilities (2nd) | Obs | 0 | 1 | 8 | 12 | 8 | 22 | 2 | 53 | 0.004 |
| Exp | 1.1 | 5.7 | 12.9 | 8.9 | 3.5 | 15.4 | 5.5 | ||||
| Cellular transport, transport facilities and transport routes | Transported compounds (2nd) | Obs | 0 | 3 | 11 | 14 | 9 | 19 | 2 | 58 | 0.024 |
| Exp | 1.2 | 6.2 | 14.1 | 9.8 | 3.9 | 16.8 | 6.0 | ||||
| Classification not yet clear-cut | Obs | 1 | 3 | 14 | 2 | 3 | 10 | 6 | 39 | 0.210 | |
| Exp | 4.2 | 5.6 | 7.0 | 4.2 | 2.8 | 13.9 | 1.4 | ||||
| Energy | Obs | 0 | 1 | 5 | 9 | 11 | 28 | 5 | 59 | 0.000 | |
| Exp | 6.3 | 8.4 | 10.5 | 6.3 | 4.2 | 21.1 | 2.1 | ||||
| Energy | Respiration (2nd) | Obs | 0 | 0 | 2 | 3 | 4 | 12 | 0 | 21 | 0.010 |
| Exp | 0.4 | 2.3 | 5.1 | 3.5 | 1.4 | 6.1 | 2.2 | ||||
| Energy | Electron transport and membrane-associated energy conservation (2nd) | Obs | 0 | 0 | 1 | 3 | 5 | 10 | 0 | 19 | 0.003 |
| Exp | 0.4 | 2.0 | 4.6 | 3.2 | 1.3 | 5.5 | 2.0 | ||||
| Interaction with the cellular environment | Obs | 2 | 5 | 15 | 8 | 4 | 14 | 1 | 49 | 0.323 | |
| Exp | 5.3 | 7.0 | 8.8 | 5.3 | 3.5 | 17.5 | 1.8 | ||||
| Protein fate (folding, modification and destination) | Obs | 2 | 11 | 28 | 13 | 6 | 38 | 11 | 109 | 0.758 | |
| Exp | 11.7 | 15.6 | 19.5 | 11.7 | 7.8 | 38.9 | 3.9 | ||||
| Protein synthesis | Obs | 0 | 2 | 15 | 60 | 0 | 6 | 2 | 85 | 0.000f | |
| Exp | 9.1 | 12.1 | 15.2 | 9.1 | 6.1 | 30.4 | 3.0 | ||||
| Protein synthesis | Ribosome biogenesis (2nd) | Obs | 0 | 1 | 6 | 49 | 0 | 0 | 0 | 56 | 0.000 |
| Exp | 1.1 | 6.0 | 13.6 | 9.4 | 3.7 | 16.2 | 5.8 | ||||
| Protein synthesis | Ribosomal protein (3rd) | Obs | 0 | 0 | 0 | 24 | 0 | 0 | 0 | 24 | 0.000 |
| Exp | 0.5 | 2.6 | 5.8 | 4.0 | 1.6 | 7.0 | 2.5 | ||||
| Protein with binding function or cofactor requirement (structural or catalytic) | Obs | 0 | 3 | 12 | 8 | 4 | 15 | 0 | 42 | 0.177 | |
| Exp | 4.5 | 6.0 | 7.5 | 4.5 | 3.0 | 15.0 | 1.5 | ||||
| Subcellular localization | Obs | 1 | 23 | 51 | 71 | 15 | 72 | 16 | 249 | 0.000f | |
| Exp | 26.7 | 35.6 | 44.5 | 26.7 | 17.8 | 88.9 | 8.9 | ||||
| Subcellular localization | Mithochondrion (2nd) | Obs | 0 | 5 | 16 | 28 | 8 | 21 | 4 | 82 | 0.002 |
| Exp | 0.8 | 4.1 | 9.3 | 6.5 | 2.6 | 11.1 | 4.0 | ||||
| Subcellular localization | Cytoplasm (2nd) | Obs | 0 | 3 | 11 | 27 | 2 | 13 | 4 | 60 | 0.000 |
| Exp | 0.8 | 4.1 | 9.3 | 6.5 | 2.6 | 11.1 | 4.0 | ||||
| Metabolism | Obs | 4 | 19 | 55 | 24 | 14 | 55 | 31 | 202 | 0.105 | |
| Exp | 21.6 | 28.9 | 36.1 | 21.6 | 14.4 | 72.1 | 7.2 | ||||
| Metabolism | Amino acid biosynthesis (2nd)e | Obs | 1 | 3 | 14 | 0 | 0 | 4 | 3 | 25 | 0.004 |
| Exp | 0.5 | 2.7 | 6.1 | 4.2 | 1.7 | 7.2 | 2.6 | ||||
| Transcription | Obs | 1 | 13 | 34 | 18 | 1 | 25 | 4 | 96 | 0.009 | |
| Exp | 10.3 | 13.7 | 17.1 | 10.3 | 6.9 | 34.3 | 3.4 | ||||
| Transcription | RNA synthesis (2nd) | Obs | 1 | 13 | 31 | 18 | 1 | 25 | 4 | 93 | 0.021 |
| Exp | 1.9 | 10.0 | 22.6 | 15.7 | 6.2 | 27.0 | 9.7 | ||||
| Unclassified proteins | Obs | 12 | 55 | 108 | 60 | 38 | 134 | 66 | 473 | 0.002f | |
| Exp | 50.7 | 67.6 | 84.5 | 50.7 | 33.8 | 168.9 | 16.9 | ||||
| Transcription factors | Tables 9–14 in (4) | Obs | 1 | 5 | 9 | 1 | 1 | 9 | 1 | 27 | 0.017 |
| Exp | 0.5 | 2.9 | 6.6 | 4.6 | 1.8 | 7.8 | 2.8 | ||||
| Heat shock proteins | Table 50 in (4) | Obs | 1 | 7 | 4 | 3 | 0 | 2 | 0 | 17 | 0.007 |
| Exp | 0.3 | 1.8 | 4.1 | 2.9 | 1.1 | 4.9 | 1.8 | ||||
| Glucan and chitin synthesis | Tables 51–52 in (4) | Obs | 0 | 2 | 2 | 1 | 0 | 4 | 1 | 10 | 0.913 |
| Exp | 0.2 | 1.0 | 2.3 | 1.6 | 0.6 | 2.8 | 1.0 | ||||
| Totalg | 26 | 138 | 313 | 217 | 86 | 373 | 134 | 1287 |
aOrdinal numbers in the parentheses indicate levels of FunCat subcategories (33).
bObserved number of genes and expected number of genes if probabilities of each outcome are independent of the cluster.
cNumber of genes in each of the subcategories.
dHypergeometric probability was used to obtain the P-value using fisher.test( ) in R (bioconductor.org).
eGenes involving in amino acid biosynthesis were selected from a MIPS subcategory ‘amino acid metabolism (2nd)’.
fChi-square test was used to obtain the P-value using chisq.test( ) in R (bioconductor.org).
gNumber of genes in each of the hierarchical clusters.