Table 2.
Cell-cycle keywords and GO terms
| Tool | G1 | S | G2 | M |
|---|---|---|---|---|
| Martini | – | True positive: (ATR-interacting protein) protein kinase complex9; Ataxia Telangiectasia9; ATR–ATRIP complex9; Claspin6; DNA polymerase alpha8; DNA replication4; eukaryotic DNA replication factor8; Fork8; Human CHL12/RFCs2-5 complex8; HUS19; novel PCNA-binding protein8; Processivities8; Proliferating cell nuclear antigen (PCNA)-binding proteins8; Replication protein A8; RFA1-T118; RP-A8; Single-stranded8; ssDNA8. Uninformative: 20 specific proteins; Double-stranded DNA; Template. | – | True positive: Anaphase15; APC/C15; Aster18; BUBR115; Centrosome18; Cytokinesis11; Interphase11; Kinetochore18; Metaphase14; Microtubule18; Midzone19; Mitotic11; Mitotic spindle18; Multinucleated16; Prometaphase13; Prophase12; Segregation15; Telophase16. Uninformative: Monopolar |
| Marmite | – | – | – | – |
| CoPub | False positive: Mitosis11; Nucleotide-excision repair5; Oogenesis. Uninformative: Adipocyte differentiation; Apoptosis; Budding; Cell adhesion; Cell cycle, death, differentiation, fate determination, fate commitment, shape; Decidualization; Dephosphorylation; Epidermal differentiation; Epithelial cell proliferation, epithelial cell differentiation; Gene silencing; Growth pattern; Histogenesis; Intracellular transport; Keratinocyte differentiation; Morphogenesis; mRNA stabilization; Nucleocytoplasmic transport; Oncogenesis; Organogenesis; Phosphorylation; Protein folding, import; Response to hypoxia; RNA interference; RNA processing; Senescence; Signal transduction; Synaptonemal complex formation, synaptogenesis; Transcription; Transduction; Translation. | True positive: Base-excision repair5; Chromatin silencing3, remodeling, modification, insulator sequence binding; DNA damage response5, metabolism2, methylation4, recombination4, repair5, replication4, synthesis2, unwinding5; Double-strand break repair5; Hyperphosphorylation3; Mismatch repair5; Nucleotide-excision repair5; Postreplication repair5; Recombination4; Recombinational repair5; Single-stranded DNA binding8; Strand displacement8; Telomere maintenance5. False positive: Division11; M phase11; Mitosis11; Meiosis chromosome segregation, meiosis; Meiosis sister chromatid cohesion, meiosis II; Meiotic recombination; Metaphase14.Uninformative: Apoptosis; ATP transport, regeneration, metabolism, hydrolysis, catabolism, biosynthesis; Budding; Cell cycle, arrest, checkpoint; Cell death, growth and/or maintenance, cell growth, proliferation; DNA amplification, fragmentation; Drug resistance; Gene conversion, expression AND epigenetic, silencing; Histone acetylation; Induction of apoptosis; Mating behavior, mating; mRNA splicing, splice site selection; Mutagenesis; Oncogenesis; Phosphorylation; Rb:E2F-1:DP-1 transcription factor; RNA interference; Senescence; Transcription, mitotic, initiation; Translation; Viral replication. | False Positive: Anaphase A and B15; Chromatin silencing3, remodeling, modification, insulator sequence binding; Chromosome condensation13, segregation15, movement; Division11; DNA damage response15, methylation4, repair5, replication4, synthesis2; M phase11; Meiosis sister chromatid cohesion, II spindle assembly, I spindle assembly, chromosome segregation; Metaphase14; Mismatch repair5; Mitosis11; Nucleotide-excision repair5; Pachytene; Prophase12; Recombination4; Spermatogenesis. Uninformative: Antigen presentation; Apoptosis; Autophosphorylation; Budding; Caspase activation; Cell cycle, arrest, checkpoint, death, invasion; Chemotaxis; Conjugation; DNA fragmentation; Dephosphorylation; Fragmentation; Gene silencing; Glutathione metabolism, conjugation reaction, catabolism, biosynthesis; Histone acetylation; Induction of apoptosis; Inflammatory response; mRNA transcription; RNA interference; Transcription, initiation. | True positive: Abscission16; Anaphase A and B15; Cell division11; Centrosome separation15, cycle; Chromosome condensation13, segregation15, movement13–15; Cytokinesis11; Division11; Envelope breakdown12; Exit from mitosis14; M phase11; Metaphase14; Metaphase–anaphase transition14; Microtubule18 processes; Mitosis11; Prometaphase13; Prophase12; Sister chromatid cohesion and separation15; Spindle elongation13, assembly13, stabilization14, checkpoint14; Telophase16. False positive: DNA replication and synthesis4; Embryonic development; Fertilization; Meiosis sister chromatid cohesion, II spindle assembly, I spindle assembly, chromosome segregation; Oocyte maturation; Oogenesis; Osteoblast differentiation; Pachytene; Spermatogenesis; ssDNA binding8. Uninformative: Adipocyte differentiation; Angiogenesis; Anti-apoptosis; Antiviral response; Apoptosis; Autophosphorylation; Budding; Caspase activation; Cell adhesion, cycle arrest, cycle checkpoint, death, differentiation, fate specification, fate determination, fate commitment, growth and-or maintenance, growth, invasion, migration, motility, polarity, proliferation, size; Cell–cell adhesion; Cytoskeleton; Dephosphorylation; DNA damage response, fragmentation, repair; Double-strand break repair; Epithelial cell proliferation, differentiation; Fibroblast proliferation; Fragmentation; G-protein signaling; G2 checkpoint; G2/M checkpoint, transition; Gastrulation; Gene expression, epigenetic, silencing; Growth; Histone acetylation, modification; Hyperphosphorylation; Induction of apoptosis; Lung development; Mammary gland development; Mevalonate transport, pathway; Migration; Morphogenesis; mRNA processing, splicing, splice site selection, transport; Myogenesis; Neurogenesis; Nucleocytoplasmic transport; Oncogenesis; Phosphorylation; Programmed cell death; Protein prenylation; RNA interference, splicing; Senescence; Signal transduction; T-cell differentiation, homeostasis; Transcription, mitotic, initiation; Transduction; Vasculogenesis; Viral replication. |
| FatiGO | False positive: M phase of mitotic cell cycle11. Uninformative: Cell cycle; Intracellular organelle (membrane-bound); Ribonucleoprotein complex. | True positive: DNA metabolic process2, repair5, replication4; DNA-dependent DNA replication4; Response to DNA damage stimulus5; Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process2; Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process2. False positive: Cell division11 Uninformative: Biopolymer metabolic process; cell communication, surface receptor linked signal transduction; cellular metabolic process; DNA binding; Hydrolase activity; intracellular membrane-bound organelle; macromolecule metabolic process; membrane-bound organelle; mitotic cell cycle; nucleic acid binding; primary metabolic process; Regulation of cellular metabolic process; regulation of metabolic process; response to endogenous stimulus; response to stress; RNA metabolic process. | – | True positive: Cell division11; M phase of mitotic cell cycle11; microtubule18-based process; mitosis11; regulation of mitosis11. False positive: DNA metabolic process2, repair5, replication4; Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process2. Uninformative: Biopolymer metabolic process; cell cycle, phase, process; cellular metabolic process; cytokine production; cytoskeleton, organization and biogenesis; macromolecule metabolic process; microtubule cytoskeleton organization and biogenesis; nucleic acid binding; primary metabolic process; response to DNA damage stimulus; response to endogenous stimulus; response to stress. |
| ProfCom | Uninformative: Hydrolase activity. | – | Uninformative: Hydrolase activity. | – |
The output of different tools applied to four gene sets, corresponding to the cell-cycle phases G1, S, G2 and M. Each output term was categorized as ‘true positive’, ‘false positive’ or ‘uninformative’. Superscripts indicate matches to the cell-cycle benchmark (Table 3). Qualitatively, Martini gave the best performance.