HuGE Navigator

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract HuGE Navigator is an integrated, searchable knowledge base (KB) of genetic associations and human genome epidemiology.

HuGE Navigator provides access to a continuously updated knowledge base in human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene-environment interactions, and evaluation of genetic tests.

The Human Genome Epidemiology Network (HuGENet™) is a voluntary, international collaboration focused on assessing the role of ‘human genome’ variation in health and disease at the population level.

Since 2001, HuGENet™ has maintained a database of published, population-based epidemiologic studies of human genes extracted and curated from PubMed.

The HuGE Navigator replaces earlier search tools for use with this database and provides additional applications for use by researchers and the public.

HuGE Navigator search tools and systems --

1) HuGEpedia - an encyclopedia of human ‘genetic variation’ in health and disease.

• a) Phenopedia - Phenopedia provides a disease-centered view of genetic association studies summarized in the online Human Genome Epidemiology (HuGE) encyclopedia. Users can switch to a gene-centered view (Genopedia) or to other HuGE Tools by using the Search dropdown list.
• b) Genopedia - Genopedia provides a gene-centered view of genetic association studies summarized in the online Human Genome Epidemiology (HuGE) encyclopedia. Users can switch to a disease- centered view (Phenopedia) or to other HuGE Tools by using the Search dropdown list.
• Note: Datasets for Phenopedia and Genopedia are available for downloading as text files via the links provided on their respective home pages.

2) HuGEtools - searching and mining the literature in human genome epidemiology.

• a) HuGE Literature Finder - HuGE Literature Finder is a ‘search engine’ for finding published literature on genetic associations and other human genome epidemiology. The search query can include disease/outcome, environmental factors, genes, author's name, affiliation, etc.
• The results can be further refined by the filtering feature. The list of selected articles can be redirected to the PubMed website to take advantage of the functionality it provides, such as uploading to reference software.
• Note: Database includes publications since 2001.
• b) HuGE Investigator Browser - HuGE Investigator Browser is a search engine for finding investigators or collaborators in genetic associations and other human genome epidemiology research based on study interests such disease/condition, environmental risk factors, or gene.
• Investigator profile information is extracted using an accessory utility that automatically parses the affiliation data provided by PubMed.
• c) Gene Prospector - Gene Prospector is a ‘bioinformatics tool’ designed to sort, rank, and display information about genes in relation to human diseases, risk factors and other phenotypes.
• Links are provided to evidence from published literature and to other online data sources. Search terms can include diseases, risk factors and phenotypes.
• d) HuGE Watch - HuGE Watch is designed for tracking the evolution of published HuGE research dynamically based on the literature repository in the database.
• It allows users to view the temporal trends and the geographical distributions of the published HuGE literature, HuGE investigators, gene studied and disease studied in HuGE field.
• e) Variant Name Mapper - Variant Name Mapper is designed to map ‘gene variant’ common names to their corresponding RefSNP accession IDs (rs numbers) using information compiled from the following open-access web sources:
• SNP500Cancer, SNPedia, pharmGKB (see G6G Abstract Number 20304), ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, Locus-Specific DataBases(LSDBs). User submissions are also welcome.
• f) HuGE Risk Translator - HuGE Risk Translator is a tool to help evaluate the predictive ability of ‘genetic markers’ by calculating a variety of indicators in epidemiology, clinical validity & utility and public health.
• Finding a ‘genetic association’ is only the first step towards translation to population health benefits. Whether a genetic marker can yield a useful predictive test depends on the frequency of the risk genotype, the ‘disease risk’ in the population and the strength of the association between the genetic marker and the occurrence of disease.
• These indicators include the genotype-specific disease risks, the sensitivity and specificity of the genetic test and the population attributing fraction, among others. The indicators can be calculated when the frequency of the risk variant, the population disease risk and the odds ratio between the gene and disease are known.

3) HuGEmix - a series of HuGE related informatics utilities and projects.

• a) GAPscreener – GAPscreener is an automatic tool for screening human genetic association literature in PubMed using the support vector machine (SVM) technique.
• GAPscreener is one of the first free SVM-based applications available for screening the human genetic association literature in PubMed with high recall and specificity.
• Note: GAPscreener has been used in the screening and curation of the HuGE Navigator database.
• b) HuGE Track - HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser (see G6G Abstract Number 20197).

System Requirements

Web-based.

Manufacturer

• Centers for Disease Control and Prevention (CDC)
• 1600 Clifton Rd.
• Atlanta, GA 30333
• USA

Manufacturer Web Site HuGE Navigator

Price Contact manufacturer.

G6G Abstract Number 20506

G6G Manufacturer Number 104125