Table 4.

Keywords for metastatic versus primary melanoma

Tool	Keywords/GO terms
Martini	Mitosis-related: Anaphase; APC/C; Arrest; Ataxia telangiectasia; BUBR1; Camptothecin; CDC20; CDH1; CDK2; CDK2 kinase; CDT1; Cell cycle; Cell division; Centrosome; Checkpoint; Chromatid; Claspin; Cohesin; Cyclin B; Cyclin-dependent; Cyclin-dependent kinases; Cyclosome; Cytogenetic; Cytokinesis; DNA damage; DNA repair; DNA replication; DNA-binding protein; Double-strand break; Double-stranded DNA; E2F transcription factor; E2F4; EGF; Elongation; Elongation factor; Fork; G2-phase; Guanine nucleotide; H2B; Helicase, Initiation factor; High-sensitive reverse transcription-nested polymerase chain; Histone; Histones; Intermediate filament; Interphase; Junctional; Kinase; Kinases; Kinetics; Kinetochore; Ligases; Ligated; M-phase; MAD1; MAD2; Metaphase; Microtubule; Midbodies; Midzone; Minichromosome; Misalignment; Missegregation; Mitotic; Mitotic spindle; Monopolar; Multipolar; Non-phosphorylatable; Nuclear antigen; Nuclear pore; Nuclear protein; Nucleolar; Nucleus; Oligoribonucleotides; PCNA; Phosphopeptides; Phosphoprotein; Phosphoproteins; Phosphorylation; Pol; Polo-like kinase 1; Polypeptide chain elongation factor 1 alpha; Posttranslational; Prometaphase; Prophase; Proteasome; Protein kinase; RAD17; rDNA; Replication; Replication protein A; Ribonucleotide; Ribosomal gene; Ribosome; Ring-shaped; RNA polymerase; RNA polymerase I subunit; RP-A; S-phase; Segregation; Small nuclear ribonucleoprotein; Small nuclear ribonucleoprotein particle; spindle associated proteins; ssDNA; Telophase; Topoisomerase; Topoisomerase I; Ubiquitin; ubiquitin ligases; Ubiquitins
	Uninformative: Assembled; Assemblies; Binaries; Biogenesis; Cerevisiae; Clade; Classification; Co-immunoprecipitation; Connection; Coordination; Cross-validation; Daughter; Degradation; Depletion; Dispensable; Dynamics; Empirical; End; Essential; Eukaryote; Eukaryotic; Eukaryotic cell; False-positive; Fraction; Global; Health; Hit; Human protein-protein; Immunodepleted; Imprinting; In-gel; Independent; Integrated; Invaluable; Lates; Layer; Leaves; Linings; Liquid chromatography-tandem mass spectrometry; Lysate; Machine; Mappings; Mass spectrometries; Matched; Mechanism; Microinjection; Motif; Motor; Multisubunit; Mus sp; Nascent; Nationals; Network; Nicotiana tabacum; Non-redundant; Oligoribonucleotide; Pairwise; Percent; Permit; Purified; Remain; Removed; Saccharomyces cerevisiae; Scale; Schizosaccharomyces; Schizosaccharomyces pombe; Spectral; Stable isotope; Stem-loop; Step; Stringent; Supplemental; Surprisingly; Systematics; Tobacco; Unlike; Unprecedented; Unsolved; Upper
	Not mitosis-related: 12 MAGE; 5′-phosphates; 941 pseudogenes; ATPase; aneuploidy; ATM kinases; Autism; Bone marrow cell; Bronchial; Calcium; Calcium-dependent; Chaperone; CHK1 protein kinase; Cornea; Cornified; Cystic fibrosis gene; Desmosome; Epidermal cell; Epithelial; Epithelial cell; Epithelium; Human gene MAGE-1; Guanine nucleotide exchange factors; Heat-shock; HSPs; Hair follicle; HeLa cell; HeLa cell nuclear; Involucrin; Keratinocyte; Lymphoid-specific; MAGE; MAGE-A; MAGE-A antigens; Melanoma antigen gene; Neurite; Novel protein-protein; Over 100 disease-associated proteins; Polyploid; Pre-rRNA; Protein complex; Proteome; PSMS; Psoriatics; Psoriasis; Pyrophosphatase; Quiescent; Rebinding; Regulatory; Repair; Reversible; single MAGE-A antigen; Site-specific; Specific kinase-substrate; Squamous epithelium; Stimuli; Stratified; Stratified epithelia; Subcellular; Subcomplex; Substrate; Subunit; Superfamilies; Suprabasal; Surface; Skin diseases; Starvation; Stratum corneum; Synthesis; Temporal; Topologies; Transmission; Unaligned; Unattached; Viral protein; Xeroderma pigmentosum
Marmite	Not mitosis-related: Psoriasis
FatiGO	Mitosis-related: Chromosome, organization and biogenesis; DNA metabolic process; E2F; M phase of mitotic cell cycle; Cell cycle, phase, process; Cell division; Chromosome segregation; DNA recombination, repair, replication; HNF1; Intermediate filament cytoskeleton; MEF-2; Mitosis, cell cycle; Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; Rb:E2F-1:DP-1; Response to DNA damage stimulus
	Not mitosis-related: Anatomical structure development, morphogenesis; Apical junction complex; Apicolateral plasma membrane; ATP binding; Biopolymer metabolic process; Cation binding; Cell adhesion, junction, part; Cellular component organization and biogenesis, metabolic process; Cornified envelope; Cytosol; Defense response; Ectoderm development; Epidermis development; Extracellular region part, space; Integral to membrane, plasma membrane; Intercellular junction; Intracellular, membrane-bound organelle; Intrinsic to membrane; Macromolecule metabolic process; Membrane-bound organelle; Multicellular organismal development; Non-membrane-bound organelle; Nuclear part; Nucleic acid binding; Nucleotide binding; Nucleus; Organ development; Organelle lumen; Plasma membrane; Primary metabolic process; Protein folding; Purine nucleotide binding; Response to endogenous stimulus; RNA binding, localization, processing; System development; Tissue development
ProfCom	—

In this table, different tools have been used to compare a set of genes associated with primary melanoma, and a second set of genes associated with metastatic melanoma. Each keyword or GO term found has been classified as either mitosis-related, uninformative, or ‘not mitosis-related’. Compared with the other tools, Martini found more keywords, more-specific keywords, but also more uninformative keywords.