Bioinformatics 101: Genomic Databases

Genomic Annotations:

• UCSC Genome Browser
• ENA - European Nucleotide Archive
• Ensembl
• database of genome annotations
• ENCODE
• NHGRI project to catalog functional elements in the human genome
• There are various data portals, including the UCSC Genome Browser
• NCBI Databases
• GenBank - NCBI genome sequence database
• Entrez Nucleotide 
• miRBase
  • miRNA database

Systems Biology Databases:

• Gene Ontology (GO)
• Database of functional annotations for protein-coding genes
• KEGG - Kyoto Encyclopedia of Genes and Genomes
• primarily used as a pathway database
• IntAct - database for protein-protein interactions
• Reactome
• Regulome Explorer - software to visualize integrative genomic data from the TCGA project
• BioGRID - database of genetic and protein interactions
• MINT - protein-protein interaction database
• STRING - database for known and predicted protein-protein interactions
• STITCH: database of drug-protein interactions

Microarray / Sequencing Databases:

• GEO - microarray database
• ArrayExpress - microarray database
• SRA - sequencing archive; entries are often also indexed in GEO
• BioGPS - similar to NCBI Gene, but also includes normal tissue expression levels (from microarray data)
• TiGER - tissue-specific gene expression database
• CellMiner - query NCI-60 cell line data
• TCGA Data Portal - integrative genomic data for large cancer datasets

Genomic Variation Databases:

• dbSNP
• database of human single nucleotide polymorphisms (SNPs)
• GWAS Catalog
• HapMap
• project to characterize human genetic variation
• Database of Genomic Variants (DGV)
• Genome Variation Server (GVS)

Disease-Centric Databases:

• General
• OMIM - Online Mendelian Inheritance in Man
• database of human diseases
• SIDER - EMBL side effect database
• Cancer
• cBioPortal
• User-friendly interface for querying cancer datasets (including TCGA data)
• TCGA - The Cancer Genome Atlas
• includes microarray and sequencing data
• Oncomine
• database of gene expression and copy number data from patients
• basic access is free, but license is required for premium access
• caArray - NCI Cancer Database

Protein Databases:

• Protein Data Bank (PDB) - database of 3D structures for proteins
• Prosite - database of protein families and domains