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Table 1 Databases used by operational modules in the GeneTerpret Platform

From: GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation

Module Task Databases
ExPhenosion Identifies genes associated with the selected phenotype(s) and its/their superclass phenotypes Human Phenotype
Ontology (HPO)
Medical Subject
Headings (MeSH)
CanGene   
 Cross-species: Mouse Identifies candidate genes that cause a “similar” phenotype in a mouse model Mouse Genome Informatics (MGI)
 Cross-species: Zebrafish Identifies candidate genes that cause a “similar” phenotype in the zebrafish model The Monarch Initiative
 Homology Identifies candidate genes homologous to known disease genes for a phenotype Ensembl
 Protein–Protein interaction Identifies candidate genes/proteins that physically interact with known disease genes/proteins based on human studies The Biological General Repository for Interaction Datasets (BioGRID)
 Gene Expression Identifies candidate genes expressed in the affected tissue EMBL-EBI Expression Atlas
Known INvolved Genes (KING) Identifies known genes for a selected phenotype Online Mendelian
Inheritance in Man (OMIM)
Orphanet
NCBI MedGen
NCBI ClinVar
Gene Validity Calculates validity scores for each gene by examining the strength of the evidence supporting a gene-disease relationship obtained from the above modules N/A
Variant Interpretation Program (VIP) Classifies variants based on their pathogenicity following the criteria proposed by the American College of Medical Geneticists (ACMG) ClinGen Dosage
Sensitivity Map
Decipher
haploinsufficiency
predictions
ExAC pLI score
ClinVar
The NHGRI-EBI Catalog
of published GWAS
Pfam clans
Weil et al. 2017 [25]
Causality Graphical visualization of the distribution of prioritized variants across the five classifications of pathogenicity GeneTerpret GUI