Table 1 Summary of disease and gene reports displayed in Gene2Function (G2F)
Column HeaderContentSource of Content
Disease report
 Gene symbol humanOfficial gene symbolNCBI gene
 Gene ID humanNCBI gene IDNCBI gene
 Count disease termsNumber of disease termsOMIM, EBI GWAS
 Disease termsDisease termsOMIM, EBI GWAS
 Ortholog overviewLink to G2F gene reportInternal
Gene report
 NCBI gene IDNCBI gene IDNCBI gene
 SymbolOfficial gene symbolNCBI gene
 Human disease countsNumber of disease terms; link to MARRVELaOMIM, EBI GWAS
 Species nameSpecies name
 Species-specific gene IDSpecies-specific gene IDLinks to HGNC or MOD gene reportb
 Species-specific databaseRelevant database nameLinks to HGNC or MOD home page
 DIOPT scoreDIOPT scorecDIOPT
 Best scoreYes or no, this pair has best score at DIOPTDIOPT
 Best score reverseYes or no, this pair has best score if opposite searchDIOPT
 ConfidenceDIOPT confidencedDIOPT
 Publication countNumber of publications on the orthologNCBI gene2pubmed
 GO component countsNumber of cellular component GO terms assigned to the orthologNCBI gene2go
 GO function countsNumber of molecular function GO terms assigned to the orthologNCBI gene2go
 GO process countsNumber of biological processes GO terms assigned to the orthologNCBI gene2go
 Protein interaction countsNumber of protein interactions assigned to the orthologBioGrid
 Genetic interaction countsNumber of genetic interactions assigned to the orthologBioGrid
 Mine phenotype dataNumber of phenotype entries from MineseHumanMine, MouseMine, XenMine, ZebrafishMine, FlyMine, WormBase, SGD
 Mine expression dataNumber of expression entries from MineseHumanMine, MouseMine, XenMine, ZebrafishMine, FlyMine, WormBase, SGD
 Mine disruption phenotypeNumber of disruption phenotype entriesUniProt
 3D structureNumber of 3D structures available for the orthologProtein data bank
 ORF clonesNumber of ORF clonesPlasmID clone repositoryf
 Protein alignmentMultiple or pairwise alignment of orthologsDIOPT
  • OMIM, Online Mendelian Inheritance in Man; EBI, European Bioinformatics Institute; GWAS, genome-wide association study; HGNC, HUGO Gene Nomenclature Committee; MOD, model organism database; DIOPT, DRSC Integrative Ortholog Prediction Tool; GO, gene ontology; SGD, Saccharomyces Genome Database; ORF, open reading frame.

  • a MARRVEL, Model organism Aggregated Resources for Rare Variant ExpLoration (Wang et al. 2017).

  • b The databases included at G2F are MGI (Blake et al. 2017), RGD (Shimoyama et al. 2015), Xenbase (Karpinka et al. 2015), ZFIN (Howe et al. 2017), FlyBase (Gramates et al. 2017), WormBase (Howe et al. 2016), SGD (Cherry et al. 2012), and PomBase (McDowall et al. 2015).

  • c DIOPT score, number of ortholog prediction tools included at DIOPT (Hu et al. 2011) that cover both species and predict the displayed ortholog match.

  • d In this column, “High” indicates that the ortholog pair has the best score among all pairs with both a forward and a reverse direction score and a DIOPT ≥ 2; “Moderate” indicates that the ortholog pair has the best score with the forward or the reverse search and a DIOPT ≥ 2, or has a DIOPT score ≥ 4 but is not the best score with either a forward or reverse search; and “Low” includes all other predicted ortholog pairs.

  • e Mines (or MODs serving that function): HumanMine, MouseMine, XenMine, ZebrafishMine, FlyMine, WormBase, and SGD (Cherry et al. 2012; Smith et al. 2012; Howe et al. 2016).

  • f Links provided for one of several repositories in the United States and overseas that have ORF clones, many of which are from the ORFeome Collaboration (2016).