Meta-databases

• BLD Bioinformatics Links Directory
• OBRC Online Bioinformatics Resources Collection
• DoD Database of Databases
• MetaDatabase Database of Biological Databases

Microarray Data

• GEO Gene Expression Omnibus
• PUMAdb Princeton University Microarray Database
• SMD Stanford Microarray Database
• ArrayExpress EBI's Array Express
• ExpressDB Harvard's ExpressDB

Interaction Data

• BIND, Biomolecular Interaction Network Database
• bioGRID, General Repository for Interaction Datasets
• DIP, Database of Interacting Proteins
• IntAct, EBI's interaction database
• MINT, Molecular INTeractions database
• MIPS PPI, Munich Information center for Protein Sequences Protein-Protein Interactions

Sequence, Sites, and Domains

• Transfac, Transcription Factor binding sites, targets, and factors
• PFAM, Protein FAMilies (curated and assigned by homology)
• SMART, Simple Modular Architecture Research Tool (protein domains)
• ProSite, ExPASy's small protein binding sites and domains

Curated References

• GO, Gene Ontology (hierarchical gene function catalog)
• KEGG, Kyoto Encyclopedia of Genes and Genomes (pathway/function catalog)
• MIPS, Munich Information center for Protein Sequences (gene function catalog)
• SGD, Saccharomyces Genome Database
• HPRD, Humap Protein Reference Database
• Reactome, curated pathway database
• OMIM, Online Mendelian Inheritance in Man (disease genes)