Bioinformatics: databasing and gene annotation

Methods Mol Biol. 2008;460:145-57. doi: 10.1007/978-1-60327-048-9_7.


"Omics" experiments amass large amounts of data requiring integration of several data sources for data interpretation. For instance, microarray, metabolomic, and proteomic experiments may at most yield a list of active genes, metabolites, or proteins, respectively. More generally, the experiments yield active features that represent subsequences of the gene, a chemical shift within a complex mixture, or peptides, respectively. Thus, in the best-case scenario, the investigator is left to identify the functional significance, but more likely the investigator must first identify the larger context of the feature (e.g., which gene, metabolite, or protein is being represented by the feature). To completely annotate function, several different databases are required, including sequence, genome, gene function, protein, and protein interaction databases. Because of the limited coverage of some microarrays or experiments, biological data repositories may be consulted, in the case of microarrays, to complement results. Many of the data sources and databases available for gene function characterization, including tools from the National Center for Biotechnology Information, Gene Ontology, and UniProt, are discussed.

MeSH terms

  • Computational Biology*
  • Databases, Genetic*
  • Databases, Protein*
  • Oligonucleotide Array Sequence Analysis