QTL Analysis Tools:

• Biomart enables the user to access information for genes or gene products based on genomic location or on a variety of individual database identitiers.  Available information includes annotations to diesease, phenotype, pathway and gene ontologies fascilitating analysis of candidate genes within a QTL region.
• QTL Matchmaker allows the user to determine if sequences of interest lie within QTL regions in a single species or across species.
  - single species
  - cross species

 

Genome Browsers:

• Rat Genome Browser In addition to the typical sequence tracks, RGD’s Genome Browser provides QTL tracks and biological tracks for diseases, phenotypes, pathways, gene function, biological process and cellular component.
• Human Genome Browser RGD also provides a human genome browser with QTL, disease, pathway, phenotype, biological process and cellular component tracks.
• GViewer Gviewer provides users with complete genome view of gene and QTL annotated to a function, biological process, cellular component, phenotype, disease, or pathway.
• UCSC Browser
• Ensembl Browser
• NCBI Browser

GO Analysis Tools:

• GOMiner GoMiner leverages the Gene Ontology to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research.
• Onto-Express , Onto-Compare , Onto-Design ,  Onto-Translate OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. Additional tools are provided for microarray data storing and analysis.