Gene expression databases (mostly microarray data) Genome databases These databases collect genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome. Phenotype databases PHI-base: pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer reviewed literature. RGD Rat Genome Database: genomic and phenotype data for Rattus norvegicus PomBase database: manually curated phenotypic data for the yeast Schizosaccharomyces pombe RNA databases miRBase: the microRNA database PolymiRTS: a database of DNA variations in putative microRNA target sites PolyQ: database of polyglutamine repeats in disease and non-disease associated proteins Rfam: a database of RNA families Amino acid / protein databases Several publicly available data repositories and resources have been developed to support and manage protein related information, biological knowledge discovery and data-driven hypothesis generation. The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other. Protein sequence databases Protein structure databases Protein Data Bank (PDB), comprising: Protein DataBank in Europe (PDBe) ProteinDatabank in Japan (PDBj) Research Collaboratory for Structural Bioinformatics (RCSB) Structural Classification of Proteins (SCOP) CATH : Protein Structure Classification database For more protein structure databases, see also Protein structure database. Protein model databases ModBase: database of comparative protein structure models (Sali Lab, UCSF) Similarity Matrix of Proteins (SIMAP): database of protein similarities computed using FASTA Swiss-model: server and repository for protein structure models AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials Protein-protein and other molecular interactions BioGRID: general repository for interaction datasets (Samuel Lunenfeld Research Institute) RNA-binding protein database Database of Interacting Proteins (Univ. of California) IntAct: open-source database for molecular interactions (EMBL-EBI) String: an open source molecular interaction database to study interactions between proteins Protein expression databases Human Protein Atlas: aims at mapping all the human proteins in cells, tissues and organs Signal transduction pathway databases NCI-Nature Pathway Interaction Database Netpath: curated resource of signal transduction pathways in humans Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute,