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. 2005 Oct 17;23(2):246-56.
doi: 10.1152/physiolgenomics.00040.2005. Epub 2005 Aug 16.

Tools and strategies for physiological genomics: the Rat Genome Database

Affiliations

Tools and strategies for physiological genomics: the Rat Genome Database

Simon N Twigger et al. Physiol Genomics. .

Abstract

The broad goal of physiological genomics research is to link genes to their functions using appropriate experimental and computational techniques. Modern genomics experiments enable the generation of vast quantities of data, and interpretation of this data requires the integration of information derived from many diverse sources. Computational biology and bioinformatics offer the ability to manage and channel this information torrent. The Rat Genome Database (RGD; http://rgd.mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative genomics, to human and mouse. We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.

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Figures

Fig. 1
Fig. 1
Overview of physiological genomics in the rat and the various translational technologies available to relate rat research to human systems. Left: traditional positional cloning techniques whereby 2 rats, 1 possessing the phenotype of interest and the other being a nonaffected control strain, are crossed, and the progeny are genotyped and phenotyped leading to the definition of quantitative trait loci (QTLs) linking the phenotype to specific regions of the genome. The regions are then examined for potential candidate genes, and comparative genomics is used to integrate evidence from other organisms or to translate results to the human genome. Translation of information to the human system is also becoming possible using informatic tools such as ontologies. Various ontologies are shown connecting elements of the experimental paradigm to related human data.
Fig. 2
Fig. 2
List of curated data contained within the Rat Genome Database (RGD). Not shown are splice variants, which are curated as a subset of genes, and rat single nucleotide polymorphism (SNP) data, which are available via the RGD Gbrowse genome browser but are not currently part of the main RGD curated database.
Fig. 3
Fig. 3
Comparison table of the tools: their functionality and applicability to the selected research tracks. A checkmark means that a tool provides the indicated functionality or is broadly applicable to projects on the indicated research track. ACP, Allele Characterization Project; BLAST, Basic Local Alignment Search Tool; BLAT, BLAST-Like Alignment Tool; VCMap, Virtual Comparative Map; RH, Radiation Hybrid.
Fig. 4
Fig. 4
Strategies for using RGD in support of positional cloning experiments. GO, Gene Ontology; SSLP, simple sequence length polymorphism.
Fig. 5
Fig. 5
Strategies for using RGD in support of comparative genomics experiments.
Fig. 6
Fig. 6
Strategies for using RGD in support of expression profiling experiments. EST, expressed sequence tag.
Fig. 7
Fig. 7
Strategies for using RGD in support of functional genomics experiments.
Fig. 8
Fig. 8
External databases and tools accessible from RGD gene records: 1) Univ. of California Santa Cruz (UCSC) Genome Browser, http://genome.ucsc.edu; 2) Mouse Genome Database, http://www.informatics.jax.org; 3) Gene Ontology (GO) Consortium, http://geneontology.org; 4) The Institute for Genomic Research (TIGR) Gene Indices, http://www.tigr.org/tdb/tgi/; 5) RatMap, http://ratmap.gen.gu.se; 6) Kyoto Encyclopedia of Genes and Genomes (KEGG), http://www.genome.jp/kegg/; 7) Universal Protein Resource (UniProt), http://www.uniprot.org/; 8) National Center for Bio-technology Information (NCBI), http://www.ncbi.nlm.nih.gov/; 9) VISTA Genome Browser, http://pipeline.lbl.gov/; 10) Ensembl, http://www.ensembl.org/; and 11) Evolutionary Conserved Region (ECR) Browser, http://ecrbrowser.dcode.org/.

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