Version 5.4

Help: Advanced Search for Genes and Proteins

This page provides the user with a number of options to search for genes or proteins of interest.

Choose organism - InnateDB contains human, mouse and bovine genes and proteins.

The default on this page is to search for proteins/genes by the protein/gene name. A search of InnateDB by the Protein/Gene name will automatically search the full gene name, all encoded protein names, the gene symbol and all synonym symbols (alternative names) for the gene. This option provides users the flexibility to find a gene/protein without having to know the HUGO name for it, which may be different from the common name(s). An exact search will be much faster and will return database entries that exactly match your query.

Several other options for searching the database are provided on this page:

  • InnateDB molecule ID: stable identifiers for a gene/protein in InnateDB (e.g. IDBG-82738 is the ID for human TLR4).
  • HUGO gene symbol/ID: Human Genome Organization Gene Nomenclature Committee official symbol or numerical ID. (For human genes only).
  • Gene Ontology (GO) Accession: search for genes/proteins that are annotated by the GO consortium as being involved in a particular function, role or localization using the GO ID number (e.g. GO:0006954 is the ID for inflammatory response).
  • Gene Ontology (GO) Term: as above but allows free-text search (e.g. inflammatory). Using exact searches is not recommended here.
  • Ensembl ID: search using a human, mouse or bovine gene, protein or transcript accession number from the Ensembl database.
  • UniProt Accession: search using an accession number from the UniProt protein database.
  • Entrez Gene ID: search using an ID number from NCBI's Entrez Gene database.
  • RefSeq Accession: search using an accession number from NCBI's RefSeq database.
  • UniGene ID: search using an ID number from NCBI's UniGene database.
  • OMIM ID: search using an ID number from the Online Mendelian Inheritance in Man database.
  • EMBL Accession: search for a particular gene/protein based on the EMBL accession number.
  • PFAM Accession: search for encoded proteins containing matching PFAM domains.
  • InterPro Accession: search for encoded proteins containing matching InterPro domains.

Choose to return Genes (default) or proteins using the "Return a list of" menu.

If you use InnateDB for your research, please cite the following publication:

Breuer et al., InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation. Nucl. Acids Res. (2013) 41 (D1) 

InnateDB is being developed jointly by the Brinkman Laboratory (Simon Fraser University, British Columbia, Canada), the Hancock Laboratory (University of British Columbia, Vancouver, British Columbia) and the Lynn EMBL Australia Group (South Australian Health & Medical Research Institute and Flinders University, Adelaide, Australia).

Funding is currently provided by Allergen and EMBL Australia. Previous funding has been provided by Genome Canada, the Foundation for the National Institutes of Health through the Grand Challenges in Global Health initiative and by Teagasc. InnateDB curated interactions are licensed under the Design Science License. All other data is licensed under the terms of the originating database. Contact: innatedb-mail@sfu.ca