Robust search capacity
Users can perform free text searches of data extracted from published GWAS. Searchable terms include the disease/trait, gene name/gene symbol/gene alias, rs number, first author name, journal, chromosome region, platform, PubMed ID, and any text in the publication title or abstract. Search results can be filtered by variant, gene, region, trait, publication, author, journal, and year, as well as by ‘hit' (ie, the SNP-trait association identified in a GWAS). Results can be filtered multiple times. The filtering function also can be used to obtain a quick snapshot of GWAS published in a particular research field. For example, a user can easily get descriptive statistics for GWAS on breast cancer, including the number of variants that have been studied, the number of GWAS publications, etc ().
Figure 1 Illustration screen shots for GWAS Integrator. (a) Display of the GWAS hits related to breast cancer. (b) Display of SNP proxies of the variants related breast cancer. (c) Display of dynamically-generated SNP and candidate gene UCSC custom tracks related (more ...)
Data mining capacity
A series of data mining capacities can be used to further explore search results.
This function provides information on SNP proxies related to the variants (SNP) of the selected GWAS hits. Users can define configuration parameters for proxy SNP retrieval, such as the HapMap release version, HapMap population, and r2 cutoff ().
This function dynamically creates an SNP custom track to display selected GWAS hits in the UCSC Genome Browser. Users can select the SNP to center the display in the UCSC Genome Browser using a dropdown menu, which lists all the rs numbers for the selected GWAS hits. The ‘Window Size' field defines the display range around the centered SNP in the UCSC Genome Browser; for example, when 500
kb is specified in the Window Size field, the UCSC Genome Browser will display 250
kb on each side of the centered SNP. Users can also include proxy SNPs in the SNP custom track, or create a separate custom track for genes indexed in the HuGE literature database related to the query ().
This function uses proxy SNPs to identify additional GWAS hits that may be related to the user-selected GWAS hits. Users can define configuration parameters for proxy SNP retrieval, such as HapMap release version, HapMap population, and r2 cutoff ().
This function lists all genes that fall into the region around the selected GWAS Hits. Users can define the genomic distance around the hits. Genes that are also indexed in the HuGE literature database and reported with the query term are highlighted with a hyperlink to the corresponding Genopedia5
record in HuGE Navigator ().
Proxy reference search
Users can also search for variant-trait associations using proxy SNPs. For example, searching with ‘rs663129' will lead to six proxy SNPs that have GWAS hits.
The statistics page presents an overview of published GWAS, including total numbers of publications, hits, reported genes, genic SNPs, intergenic SNPs, variants, and disease/traits. Temporal trends are displayed graphically for each item. A top 10 list is generated and displayed in web tables, including variant, gene, chromosome region, disease/trait, first author, and journal. As of 10 February 2011, the database contains 4817 GWAS hits, representing 475 disease/traits and 3920 variants from 796 publications.