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 and SNP tracks to facilitate the search for candidate variations that might be linked to a disease or phenotype. Gene and QTL tracks link to RGD's records, giving convenient access to a wide range of biological information.
- GViewer Gviewer provides users with complete genome view of genes and QTLs annotated to a function, biological process, cellular component, phenotype, disease, or pathway.
- VCMap The Virtual Comparative Map allows users to explore and compare genomic regions, genes and QTLs across six different species: rat, mouse, human, cow, pig and chicken.
- 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.
