Table 1.
Database | Data | URL |
---|---|---|
Variant databases | ||
1000 Genomes | Whole genome and variants of >2500 individuals | http://www.internationalgenome.org |
ClinVar | Human variants with clinical significance | https://www.ncbi.nlm.nih.gov/clinvar |
COSMIC | Catalogue of somatic mutations in cancer | https://cancer.sanger.ac.uk/cosmic |
dbSNP | Small variants from several organisms | https://www.ncbi.nlm.nih.gov/snp |
GWAS Catalog | Disease-associated variants from published GWAS | https://www.ebi.ac.uk/gwas |
SwissVar | Annotated single amino acid variants | https://swissvar.expasy.org |
Network resources | ||
BioPlex | Human PPIs from AP-MS | http://bioplex.hms.harvard.edu |
HuRI | Human PPIs from Y2H | http://interactome.baderlab.org/ |
IntAct | Manually curated PPIs from literature | https://www.ebi.ac.uk/intact |
iRefIndex | Integration of PPIs from many databases | http://irefindex.org |
KEGG | Reference database for biochemical pathways | https://www.genome.jp/kegg |
NDEx | Platform for sharing and analyzing biological networks | http://www.ndexbio.org |
Pathway Commons | Human PPIs and pathways from different sources | http://www.pathwaycommons.org |
Reactome | Integration of PPIs and pathways from many databases | https://reactome.org |
STRING | Experimental and predicted PPIs | https://string-db.org |
Disease/Phenotype association and classification | ||
CTD | Curated gene and chemical-phenotype associations | http://ctdbase.org |
Disease Ontology | Hierarchical ontology for description of diseases. | http://disease-ontology.org |
DisGeNet | Resource of variant and gene association to disease | http://www.disgenet.org |
dSysMap | Maps of disease mutations on the structural interactome | https://dsysmap.irbbarcelona.org |
HPO | Ontology for the description of phenotypic abnormalities | https://hpo.jax.org |
OMIM | Database of genes implicated in Mendelian disorders | https://omim.org |
AP-MS: affinity purification-mass spectroscopy. PPI: Protein-Protein Interaction. Y2H: Yeast two-Hybrid