Data Sourcesⓘ
Gene
| NCBI Gene | NCBI Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome, phenotype and locus-specific resources worldwide. |
| The Human Protein Atlas: Tissue | This resource of the Human Protein Atlas focuses on the expression profiles in human tissues of genes both on the mRNA and protein level. |
| MIM | MIM (Mendelian Inheritance in Man) is a comprehensive catalog of mendelian traits and disorders, human genes, and genetic phenotypes that served as the precursor to the online OMIM database. |
| HGNC | HUGO Gene Nomenclature Committee (HGNC), is a comprehensive and authoritative resource that provides unique and standardized names and symbols for all known human genes. |
| e!Ensembl | Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. |
Disease
| DisGeNet | DisGeNET is a free, comprehensive knowledge platform for human gene-disease and variant-disease associations. |
| ClinVar | ClinVar is a public archive that collects and freely provides information on human genetic variations, their associated phenotypes, and supporting evidence. |
| Human Phenotype Ontology | The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. |
| OMIM | OMIM (Online Mendelian Inheritance in Man) is a comprehensive, authoritative, and freely available compendium of human genes and genetic phenotypes. |
| Orphanet | Orphanet is a comprehensive and freely accessible global knowledge base dedicated to providing expert-validated information on rare diseases and orphan drugs. |
| ClinGen | ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. |
| PsyGeNET | PsyGeNET (Psychiatric disorders and Genes association NETwork) is a knowledge platform for the exploratory analysis of psychiatric diseases and their associated genes. |
| CBGDA | CBGDA (CRISPR-Based Gene-Disease Associations) is a database and resource dedicated to the key host genes involved in the pathogenesis of different diseases identified through genome-wide CRISPR screens. |
| LHGDN | Literature-derived Human Gene-Disease Network (LHGDN) is a knowledge base focused on human gene-disease associations extracted from scientific literature. |
| GARD | The Genetic and Rare Diseases (GARD) database, maintained by the National Institutes of Health (NIH), is a trusted public health resource that provides free, easy-to-understand, and up-to-date information on rare and genetic diseases. |
| NORD | National Organization for Rare Disorders, serves as a comprehensive and trusted resource that unites care, research, policy, and community support to empower individuals and families affected by rare diseases. |
Pathway
| KEGG | KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. |
| Reactome | Reactome is a free, open-source, and peer-reviewed online database of human biological pathways and processes. |
Protein
| UniProt | UniProt (Universal Protein Resource) is a comprehensive, high-quality, and freely accessible global resource for protein sequence and functional information. |
| STRING | STRING is a database of known and predicted protein-protein interactions. |
| Pfam | Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). |
SNP
| dbSNP | dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions. |
Gene Ontology
| Gene Ontology | The Gene Ontology (GO) project provides free, structured, controlled vocabularies for annotating genes, gene products, and sequences in molecular and cellular biology. |
miRNA
| miRTarBase | miRTarBase is a comprehensive, experimentally validated database that focuses on microRNA-target interactions (MTIs). |
Transcription factor
| TRRUST v2 | It is a manually curated database of human and mouse transcriptional regulatory networks. |
Drug
| DGIdb | Drug-Gene Interaction Database (DGIdb) streamlines the search for druggable therapeutic targets through the aggregation, categorization, and curation of drug and gene data from publications and expert resources. |
Literature
| PubMed | Database of biomedical and life science literature maintained by NCBI. |
Curation
| MeSH | MeSH (Medical Subject Headings) is a controlled, hierarchical vocabulary from the National Library of Medicine, used for indexing and searching biomedical information in databases like MEDLINE/PubMed. |
| Medline | MEDLINE is the National Library of Medicine's (NLM) premier bibliographic database that contains references to journal articles in life sciences, with a concentration on biomedicine. |