Detailed data on naturally-occurring human mutations and the phenotypes they cause are scattered among literature articles and/or individual databases dedicated to a specific gene or disease. PhenCode aims to connect these locus-specific databases (LSDBs) and make it easy to compare their data with the kinds of genotypic and functional data available at the browsers. With PhenCode, Genome Browser users can find interesting mutations and follow links back to the LSDBs for more detailed information. Conversely, LSDB users can start with queries on mutations or phenotypes and then display the results at the Genome Browser to view complementary information, such as chromatin modifications and protein binding from the ENCODE consortium. Furthermore, users will be able to query on phenotype across loci (e.g. all mutations that cause anemia, regardless of gene).
PhenCode is implemented as two custom tracks for the Genome Browser, Locus Variants and Swiss-Prot Variants, with a companion resident track containing regulatory annotations from ORegAnno. It is updated regularly from the source LSDBs, who continue to curate their data. Seamless, bi-directional connections between LSDBs and the Genome Browser allow users to explore phenotypes associated with functional elements, and to look for genomic data that could help to explain clinical phenotypes.