Table 2 Comparison of sorted class list against GENERATOR clustering with H2O2 dataset. The table shows the sorted list of over-represented functional classes for H2O2 dataset. Only the 25 best scoring classes are shown to limit the size. Columns indicate the obtained log-p-values (O.log(p)), class names and its rank in the list, and the corresponding GENERATOR cluster number, if the class was included into the obtained GENERATOR result. Notice that the most of the functional classes are associated with mitochondrial ribosome proteins. Detailed results are shown in table 7 [see Additional file 7].
From: Theme discovery from gene lists for identification and viewing of multiple functional groups
Rank | Class name | O.log(p) | In cluster |
|---|---|---|---|
1 | Mitochondrion | 40.06 | first level |
2 | mitochondrial matrix | 30.45 | II |
3 | organellar ribosome | 26.09 | II |
4 | mitochondrial ribosome | 26.09 | II |
5 | protein biosynthesis | 21.69 | II |
6 | organellar large ribosomal subunit | 18.61 | II |
7 | mitochondrial large ribosomal subunit | 18.61 | II |
8 | macromolecule biosynthesis | 15.6 | not reported |
9 | structural constituent of ribosome | 14.84 | II |
10 | Ribosome | 14.53 | II |
11 | Biosynthesis | 13.15 | not reported |
12 | structural molecule activity | 12.87 | not reported |
13 | ribonucleoprotein complex | 12.52 | II |
14 | protein metabolism | 12.34 | not reported |
15 | Metabolism | 11.75 | not reported |
16 | large ribosomal subunit | 11.33 | not reported |
17 | organellar small ribosomal subunit | 7.94 | not reported |
18 | mitochondrial small ribosomal subunit | 7.94 | not reported |
19 | aerobic respiration | 7.3 | IV |
20 | cellular respiration | 7.03 | not reported |
21 | Cytoplasm | 7.02 | not reported |
22 | RNA ligase activity | 6.68 | III |
23 | tRNA ligase activity | 6.68 | III |
24 | ligase activity, forming aminoacyl-tRNA and related compounds | 6.68 | III |
25 | ligase activity, forming carbon-oxygen bonds | 6.68 | III |