Table 3.
Cell-cycle benchmark and score-card
| Cell-cycle phases, processes and components |
Martini | Marmite | CoPub | FatiGO | ProfCom | |
|---|---|---|---|---|---|---|
| Synonyms/related genes | ||||||
| 1. G1-Phase | Gap 1 | |||||
| 2. S-Phase | DNA metabolism, synthesis; synthesis phase | 1 | 1 | |||
| Sub-processes: | 1 | |||||
| (i) Replication initiation | Chromatin silencing; Hyperphosphorylation | |||||
| (ii) DNA replication | DNA methylation, synthesis, recombination | 1 | 1 | 1 | ||
| (iii) DNA repair | Base-excision repair; DNA damage response, unwinding; double-strand break repair; mismatch repair; nucleotide-excision repair; post-replication repair; Telomere maintenance | 1 | 1 | |||
| Key components: | ||||||
| (i) Origin of replication complex | Claspin; ORC | |||||
| (ii) Mini-chromosome maintenance complex | MCM2-7 | |||||
| (iii) Replication fork | CHL12; DNA ligase; DNA polymerase; DNA replication factor; Helicase; holoenzyme; lagging strand; leading strand; Okazaki fragments; PCNA; PCNA-binding protein; pre-replication complex; primase; processivity; replication protein A (RP-A); replication factor C (RFC); single-stranded DNA; ssDNA-binding proteins; Strand displacement; Topoisomerase. | 1 | 1 | |||
| 3. DNA repair proteins | Ataxia Telangiectasia mutated gene (ATM), ATR, ATR-interacting proteins; ATRIP; CHK1 kinase, CHK2 kinase; HUS1 | 1 | ||||
| 4. G2-Phase | Gap 2 | |||||
| 5. M-Phase | Cell division; ‘Karyokinesis and cytokinesis’; Mitosis; Mitotic division; ‘Not interphase’ | 1 | 1 | 1 | ||
| Sub-processes: | 1 | 1 | ||||
| (i) Prophase | Envelope breakdown. | |||||
| (ii) Prometaphase | Chromosome condensation; spindle assembly; spindle elongation | 1 | 1 | |||
| (iii) Metaphase | BubR1; chromosome alignment; hyperphosphorylation; metaphase–anaphase transition; mitotic checkpoint; mitotic exit checkpoint; mitotic spindle checkpoint; spindle stabilization | 1 | 1 | |||
| (iv) Anaphase | APC/C; centrosome separation; chromatid separation; chromosome segregation; sister chromatid separation | 1 | 1 | |||
| (v) Telophase | Multinuclear | 1 | 1 | |||
| (vi) Cytokinesis | Abscission | 1 | ||||
| Key components: | 1 | 1 | 1 | |||
| (i) Mitotic spindle | Aster; centrosomes; centriole pair; Kinetochore; microtubules; mitotic center | |||||
| (ii) Metaphase plate | Midzone | 1 | ||||
| (iii) Cleavage furrow | Contractile ring; non-muscle myosin II+actin filaments | |||||
| True Positives (non-redundant) | 12 | 0 | 12 | 5 | 0 | |
| False Negatives | 8 | 20 | 8 | 15 | 20 | |
| False Positives | 0 | 0 | 58 | 6 | 0 | |
| Recall | 60% | 0% | 60% | 25% | 0% | |
| Precision | 100% | – | 17% | 46% | – | |
This table lists 20 key features of the human cell cycle, and uses this feature list as a benchmark to compare the performance of different tools based on their output (Table 2).