Phenopedia provides a disease-centered view of genetic association studies. Information about genes studied in relation to a particular disease (e.g. stroke) or phenotype (e.g. hypertension) is summarized on the web page in tabular format. To perform a search, the user enters a disease term in the search box; the system maps the search text onto possible MeSH disease term(s), and the user selects from among all possible terms. Results of the search include: (i) the number of published genetic association studies, including the numbers of meta-analyses and genome-wide association studies (GWAS); (ii) the number of genes studied; (iii) the number of investigators (published authors) in the field; and (iv) temporal and geographic publication trends. A separate table displays a list of genes in descending order of the frequency with which they have been studied for association with the disease. For each gene, the table includes the total number of publications, as well as the numbers of meta-analyses, GWAS and gene–environment interaction studies; a link leads to a display of publication trends for the specific gene–disease association (Supplementary Fig. 1
A and D). Each number in the table is a hyperlink that leads to a corresponding detailed information page. For example, the link for the number of publications links to results for the relevant query in HuGE Literature Finder, one of the other applications in HuGE Navigator.
We applied the method developed by Goh et al.
) to build a literature-based disease–gene network in which two diseases are ‘connected’ if they have been studied for association with the same gene(s). For a given disease, the display page lists each connected disease and the genes studied for association with both diseases (Supplementary Fig. 1
B); data are shown in tabular form, without graphic representation. In addition, genes in the tables can be grouped according to pathways defined in KEGG (Supplementary Fig. 1
C). The summary page provides links to some major disease-specific databases and published field synopses (Khoury et al.
) if available.
Similarly, Genopedia provides a gene-centered summary view of genetic association studies. The system translates a gene name, gene symbol, gene alias or protein name entered by the user into a HUGO gene symbol. Genopedia displays information about diseases that have been studied in association with a given gene using a format similar to that described for Phenopedia (Supplementary Fig. 2
A). A gene–disease network is also generated by defining two genes as ‘connected’ if they have been studied for association with the same disease(s) (Goh et al.
). The list of connected genes is displayed along with the disease(s) that connect them (Supplementary Fig. 2
B). Each search result page provides links to the foremost gene-centered databases, including NCBI Entrez Gene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=gene
), GeneCards (http://www.genecards.org/
), PharmGKB (http://www.pharmgkb.org/
) and ALFRED (http://alfred.med.yale.edu/
). Genopedia has also become a major resource linkout for these major gene-centered databases.
As of June 2009, the HuGE Navigator database contains 2506 disease MeSH terms and 5456 genes. Phenopedia and Genopedia search results (a list of genes or a list of diseases) and whole datasets for the connections between genes and diseases are downloadable in a tab-delimited text file format. Both applications are components of HuGE Navigator, which allows navigation among all components as needed.