The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.
Bottom Line: Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains.Data are submitted by researchers, acquired through bulk data pipelines or curated from published literature.Innovative software tools provide users with an integrated platform to query, mine, display and analyze valuable genomic and phenomic datasets for discovery and enhancement of their own research.
Affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA email@example.com.Show MeSH
Related in: MedlinePlus
Mentions: The Gene Annotator or GA Tool is a one-stop functional analysis tool for rat, human and mouse genes. For any of the three organisms, users can upload a list of common identifiers from RGD, EntrezGene, GenBank, Ensembl and Affymetrix or search by a chromosomal region or functional ontology identifiers to retrieve comprehensive reports for each gene. The output (Figure 6, top left) contains data related to disease and phenotype, pathway, Gene Ontology, and drug or chemical interactions, as well as dozens of identifiers and links to other sources. Functional analysis of the entire gene list or subsets can be accomplished through the Annotation Distribution Tool and the Comparison Heat Map. The Annotation Distribution Tool (Figure 6, bottom left) provides a dynamic assessment of the functional make-up of the gene list, showing the percentage of genes associated with various diseases, pathways, biological processes and functions. Users can retrieve the genes associated with a particular disease, pathway or function and further analyze this subset for functional commonalities. The tool also facilitates the retrieval of genes associated with multiple functional categories, such as those associated with a particular disease, a set of pathways and a class of drugs. The Comparison Heat Map (Figure 6, top right) visualizes the distribution of genes across two functional parameters such as disease and pathway. Users can choose the ontologies displayed on the X and Y axes and see the number of genes from their original list in the intersection of classes from each of the categories. Leveraging the power of the ontologies, users can expand each category with a click to return more specific categories and the genes with annotations in the cross-section of these. The Genome Plot (Figure 6, bottom right) provides a genome-wide view of positions for genes in the set, as well as the ability to overlay other data such as QTL, in order to see the overlap. For reference, chromosomal positions are listed in a table below the image. The plot also provides direct links to GBrowse where users can add other tracks such as SNPs, QTL, disease or transcripts. Links from the Variant Visualizer and GBrowse to the reports in the GA Tool provide direct access to comprehensive multiorganism functional profiles.
Affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA firstname.lastname@example.org.