Table 2. Evaluation of predictions made by CG-TARGET, and comparison to a baseline enrichment approach, for literature-derived, gold-standard compound-process annotations.
The target bioprocess rank was determined by its position in the list of all bioprocess predictions for each gold-standard compound, with the significance computed empirically by shuffling the bioprocesses and re-computing the rank (bold p-values indicate significance, p < 0.05). Asterisks indicate cases in which the false discovery rate of the gold-standard compound-process prediction was less than 25%. The “top-20 enrichment” approach was selected as a baseline for comparison. The “effective rank” of a compound-bioprocess prediction represents the top rank within the compound’s list of predictions among bioprocesses that are similar to the original bioprocess.
| CG-TARGET | top-20 enrichment | |||||||
|---|---|---|---|---|---|---|---|---|
| Compound | GO ID | GO term | Target process rank | Rank significance | Effective rank | Target process rank | Rank significance | Effective rank |
| 5-Fluorocytosine | GO:0032774 | RNA biosynthetic process | 27 | 0.0208 | 2 | 3 | 0.0027 | 1 |
| Aclacinomycin A | GO:0071103 | DNA conformation change | 1 | *0.0009 | 1 | 86 | 0.0643 | 2 |
| Acriflavine | GO:0006259 | DNA metabolic process | 30 | *0.0238 | 1 | 5 | 0.0042 | 1 |
| Benomyl | GO:0007017 | microtubule-based process | 2 | *0.0015 | 2 | 8 | 0.0056 | 2 |
| Blasticidin S | GO:0006412 | translation | 772 | 0.5842 | 57 | 1311 | 0.9883 | 247 |
| Bortezomib | GO:0030163 | protein catabolic process | 3 | 0.0026 | 1 | 8 | 0.0084 | 1 |
| Brefeldin A | GO:0006888 | ER to Golgi vesicle-mediated transport | 565 | 0.4207 | 32 | 1172 | 0.8818 | 169 |
| Caffeine | GO:0031929 | TOR signaling cascade | 1 | *0.0007 | 1 | 1 | 0.0007 | 1 |
| Calcofluor White | GO:0071554 | cell wall organization or biogenesis | 624 | 0.4675 | 90 | 1127 | 0.8526 | 176 |
| Camptothecin | GO:0071103 | DNA conformation change | 16 | *0.0114 | 4 | 6 | 0.0040 | 1 |
| Cisplatin | GO:0006260 | DNA replication | 134 | 0.1018 | 23 | 10 | 0.0071 | 1 |
| Daunorubicin | GO:0006260 | DNA replication | 70 | 0.0530 | 21 | 1210 | 0.9092 | 178 |
| FK228 | GO:0006325 | chromatin organization | 23 | *0.0169 | 2 | 17 | 0.0131 | 2 |
| Fluconazole | GO:0008202 | steroid metabolic process | 114 | 0.0870 | 12 | 708 | 0.5333 | 187 |
| Furazolidone | GO:0006260 | DNA replication | 20 | *0.0148 | 4 | 5 | 0.0034 | 1 |
| Gramicidin S | GO:0071554 | cell wall organization or biogenesis | 286 | 0.2186 | 39 | 1151 | 0.8705 | 173 |
| Griseofulvin | GO:0007017 | microtubule-based process | 1291 | 0.9718 | 227 | 750 | 0.5673 | 216 |
| Haloperidol | GO:0008202 | steroid metabolic process | 5 | *0.0035 | 2 | 37 | 0.0279 | 6 |
| Hedamycin | GO:0006281 | DNA repair | 4 | *0.0029 | 1 | 3 | 0.0022 | 1 |
| Hydroxyurea | GO:0006260 | DNA replication | 29 | 0.0239 | 6 | 1236 | 0.9269 | 1 |
| Itraconazole | GO:0008202 | steroid metabolic process | 234 | 0.1786 | 29 | 696 | 0.5239 | 193 |
| Latrunculin B | GO:0007010 | cytoskeleton organization | 11 | *0.0083 | 1 | 8 | 0.0068 | 2 |
| Micafungin | GO:0071554 | cell wall organization or biogenesis | 495 | 0.3718 | 47 | 1134 | 0.8577 | 150 |
| Mitomycin | GO:0006260 | DNA replication | 15 | 0.0104 | 4 | 2 | 0.0014 | 1 |
| MMS | GO:0006281 | DNA repair | 3 | *0.0022 | 1 | 3 | 0.0022 | 1 |
| Mycophenolic acid | GO:0006259 | DNA metabolic process | 1 | *0.0006 | 1 | 3 | 0.0025 | 1 |
| Nigericin | GO:0048193 | Golgi vesicle transport | 157 | 0.1158 | 13 | 1 | 0.0007 | 1 |
| Nocodazole | GO:0007017 | microtubule-based process | 2 | *0.0015 | 2 | 14 | 0.0100 | 3 |
| Oligomycin A | GO:0009268 | response to pH | 9 | 0.0075 | 2 | 2 | 0.0012 | 1 |
| Podophyllotoxin | GO:0007017 | microtubule-based process | 53 | 0.0411 | 6 | 800 | 0.6038 | 157 |
| Polyoxin D | GO:0071554 | cell wall organization or biogenesis | 1302 | 0.9788 | 225 | 1168 | 0.8828 | 173 |
| Rapamycin | GO:0031929 | TOR signaling cascade | 156 | 0.1140 | 8 | 422 | 0.3117 | 9 |
| Trichostatin A | GO:0006325 | chromatin organization | 23 | *0.0169 | 3 | 24 | 0.0173 | 1 |
| Tunicamycin | GO:0070085 | glycosylation | 1 | *0.0005 | 1 | 1 | 0.0005 | 1 |
| Tyrocidine B | GO:0071554 | cell wall organization or biogenesis | 5 | *0.0040 | 1 | 2 | 0.0019 | 1 |
| Num with significant rank | 22 | 21 | ||||||
| Num with significant rank and FDR < 25% | 16 | 0 | ||||||