Table 1 Databases used by operational modules in the GeneTerpret Platform

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