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The Rat Genome Database 2013--data, tools and users.

Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ - Brief. Bioinformatics (2013)

Bottom Line: The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators.Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website.The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.

View Article: PubMed Central - PubMed

Affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA. slaulederkind@mcw.edu

ABSTRACT
The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers. Currently, RGD combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through the organismal level. Those users access RGD from all over the world. End users are not only rat researchers but also researchers working with mouse and human data. Translational research is supported by RGD's comparative genetics/genomics data in disease portals, in GBrowse, in VCMap and on gene report pages. The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators. Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website. The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.

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Related in: MedlinePlus

Rat GBrowse. The rat Ptgs1 gene and two other genes are shown on chromosome 3 with the mouse and human synteny blocks from chromosomes 2 and 9, respectively, which indicates where the human and mouse orthologs of these particular rat genes are located.
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bbt007-F2: Rat GBrowse. The rat Ptgs1 gene and two other genes are shown on chromosome 3 with the mouse and human synteny blocks from chromosomes 2 and 9, respectively, which indicates where the human and mouse orthologs of these particular rat genes are located.

Mentions: The genome tool GBrowse [12, 20–22] affords another opportunity to analyze and compare the genetics/genomics of rat, mouse and human orthologs. RGD has three interconnected GBrowse tools specifically for rat, mouse and human genome assemblies. The rat version of GBrowse can show subsets of rat genes, QTLs and single-nucleotide polymorphisms (SNPs). Rat GBrowse also has human and mouse synteny blocks to allow quick comparison of homologous segments between rat, mouse and human chromosomes (Figure 2). The user can select one of the synteny tracks and switch the viewer to mouse or human GBrowse via a pop-up window and then view the other two species as synteny blocks.Figure 2:


The Rat Genome Database 2013--data, tools and users.

Laulederkind SJ, Hayman GT, Wang SJ, Smith JR, Lowry TF, Nigam R, Petri V, de Pons J, Dwinell MR, Shimoyama M, Munzenmaier DH, Worthey EA, Jacob HJ - Brief. Bioinformatics (2013)

Rat GBrowse. The rat Ptgs1 gene and two other genes are shown on chromosome 3 with the mouse and human synteny blocks from chromosomes 2 and 9, respectively, which indicates where the human and mouse orthologs of these particular rat genes are located.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3713714&req=5

bbt007-F2: Rat GBrowse. The rat Ptgs1 gene and two other genes are shown on chromosome 3 with the mouse and human synteny blocks from chromosomes 2 and 9, respectively, which indicates where the human and mouse orthologs of these particular rat genes are located.
Mentions: The genome tool GBrowse [12, 20–22] affords another opportunity to analyze and compare the genetics/genomics of rat, mouse and human orthologs. RGD has three interconnected GBrowse tools specifically for rat, mouse and human genome assemblies. The rat version of GBrowse can show subsets of rat genes, QTLs and single-nucleotide polymorphisms (SNPs). Rat GBrowse also has human and mouse synteny blocks to allow quick comparison of homologous segments between rat, mouse and human chromosomes (Figure 2). The user can select one of the synteny tracks and switch the viewer to mouse or human GBrowse via a pop-up window and then view the other two species as synteny blocks.Figure 2:

Bottom Line: The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators.Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website.The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.

View Article: PubMed Central - PubMed

Affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA. slaulederkind@mcw.edu

ABSTRACT
The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers. Currently, RGD combines genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through the organismal level. Those users access RGD from all over the world. End users are not only rat researchers but also researchers working with mouse and human data. Translational research is supported by RGD's comparative genetics/genomics data in disease portals, in GBrowse, in VCMap and on gene report pages. The impact of RGD also goes beyond the traditional biomedical researcher, as the influence of RGD reaches bioinformaticians, tool developers and curators. Import of RGD data into other publicly available databases expands the influence of RGD to a larger set of end users than those who avail themselves of the RGD website. The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.

Show MeSH
Related in: MedlinePlus