Table 3 Results from GENERATOR with itraconanzole dataset using five clusters. The table presents the reported classes from GENERATOR clustering with six clusters shown in figure 3. Columns and abbreviations are the same as in table 1. A more detailed view is presented in table 6 [see Additional file 6]. We omit the classes with S.log(p) smaller than 1 from the comparison with SGD (-). One outlier cluster is also omitted (shown in more detailed view).
From: Theme discovery from gene lists for identification and viewing of multiple functional groups
CLUSTER | FUNCTIONAL CLASS | C.log(p) | O.log(p) | S.log(p) | SGD |
|---|---|---|---|---|---|
I | amino acid metabolism | 51.48 | 14.7 | 38.32 | BP |
carboxylic acid metabolism | 50.64 | 14.77 | 36.64 | BP | |
organic acid metabolism | 50.64 | 14.77 | 36.64 | BP | |
amino acid and derivative metabolism | 50.36 | 13.75 | 38.32 | BP | |
amino acid biosynthesis | 49.98 | 19.07 | 31.6 | BP | |
II | steroid metabolism | 19.83 | 8.89 | 11.36 | BP |
lipid biosynthesis | 17.88 | 5.24 | 14.07 | BP | |
lipid metabolism | 17.87 | 5.05 | 13.81 | BP | |
sterol metabolism | 17.3 | 8.02 | 9.61 | BP | |
steroid biosynthesis | 16.95 | 7.69 | 9.61 | BP | |
III | plasma membrane | 9.08 | 2.58 | 7.5 | Missing |
cell wall (sensu Fungi) | 4.18 | 4.37 | 1.43 | CC | |
cell wall | 4.18 | 4.37 | 1.43 | CC | |
external encapsulating structure | 4.18 | 4.37 | 1.43 | CC | |
structural constituent of cell wall | 3.97 | 2.23 | 1.8 | Missing | |
IV | cell wall (sensu Fungi) | 2.4 | 4.37 | 0.54 | - |
cell wall | 2.4 | 4.37 | 0.54 | - | |
external encapsulating structure | 2.4 | 4.37 | 0.54 | - | |
acid phosphatase activity | 1.25 | 3.1 | 0.22 | - | |
V | specific RNA polymerase II transcription factor activity | 10.18 | 3.24 | 7.48 | MF |
nucleobase metabolism | 3.26 | 2.85 | 1.52 | Missing | |
purine base metabolism | 2.56 | 2.58 | 1.09 | Missing | |
aromatic compound metabolism | 2.54 | 5.85 | 0.72 | - | |
heterocycle metabolism | 2.22 | 2.65 | 1.02 | Missing |