Table 1. Summary of disease and gene reports displayed in Gene2Function (G2F).
| Column Header | Content | Source of Content |
|---|---|---|
| Disease report | ||
| Gene symbol human | Official gene symbol | NCBI gene |
| Gene ID human | NCBI gene ID | NCBI gene |
| Count disease terms | Number of disease terms | OMIM, EBI GWAS |
| Disease terms | Disease terms | OMIM, EBI GWAS |
| Ortholog overview | Link to G2F gene report | Internal |
| Gene report | ||
| NCBI gene ID | NCBI gene ID | NCBI gene |
| Symbol | Official gene symbol | NCBI gene |
| Human disease counts | Number of disease terms; link to MARRVELa | OMIM, EBI GWAS |
| Species name | Species name | |
| Species-specific gene ID | Species-specific gene ID | Links to HGNC or MOD gene reportb |
| Species-specific database | Relevant database name | Links to HGNC or MOD home page |
| DIOPT score | DIOPT scorec | DIOPT |
| Best score | Yes or no, this pair has best score at DIOPT | DIOPT |
| Best score reverse | Yes or no, this pair has best score if opposite search | DIOPT |
| Confidence | DIOPT confidenced | DIOPT |
| Publication count | Number of publications on the ortholog | NCBI gene2pubmed |
| GO component counts | Number of cellular component GO terms assigned to the ortholog | NCBI gene2go |
| GO function counts | Number of molecular function GO terms assigned to the ortholog | NCBI gene2go |
| GO process counts | Number of biological processes GO terms assigned to the ortholog | NCBI gene2go |
| Protein interaction counts | Number of protein interactions assigned to the ortholog | BioGrid |
| Genetic interaction counts | Number of genetic interactions assigned to the ortholog | BioGrid |
| Mine phenotype data | Number of phenotype entries from Minese | HumanMine, MouseMine, XenMine, ZebrafishMine, FlyMine, WormBase, SGD |
| Mine expression data | Number of expression entries from Minese | HumanMine, MouseMine, XenMine, ZebrafishMine, FlyMine, WormBase, SGD |
| Mine disruption phenotype | Number of disruption phenotype entries | UniProt |
| 3D structure | Number of 3D structures available for the ortholog | Protein data bank |
| ORF clones | Number of ORF clones | PlasmID clone repositoryf |
| Protein alignment | Multiple or pairwise alignment of orthologs | DIOPT |
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.
MARRVEL, Model organism Aggregated Resources for Rare Variant ExpLoration (Wang et al. 2017).
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).
DIOPT score, number of ortholog prediction tools included at DIOPT (Hu et al. 2011) that cover both species and predict the displayed ortholog match.
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.
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).
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).