Rat Genome Database
Update Report
April 2009
Genomic Elements
The Rat Genome Database continues to update genomic data regularly through
automated data import pipelines from EntrezGene and the International Protein Index. In
addition QTL and strain data are acquired through literature curation. Current figures for
data elements can be found in the table below.
2005
Rat Genes
Known Genes
Pseudogenes
Human Genes
Mouse Genes
Rat QTLs
Human QTLs
Strains
Rat SSLPs
References
8442
3432
4101
808
152
738
9730
11,651
March
2009
35,427
27,782
7492
26,703
35,351
1552
1588
1876
12,813
27,641
Biological Annotations
RGD standardizes biological annotations using four ontologies: Gene Ontology,
Mammalian Phenotype Ontology, Pathway Ontology and a disease vocabulary based on
MeSH. To provide broad-based functional information across the genome as well as indepth biological data on areas of most interest both manual literature curation and
automated pipelines are used. RGD continues to provide both broad functional genome
annotation as well as in-depth biological annotations for targeted datasets related to
particular diseases, pathways and gene families.
2005
Number of Genes with GO
annotations
Number of genes with
experimentally supported
GO
Number of GO annotations
Number of genes with
pathway annotations
Number of pathway
annotations
3850
March
2009
17,167
2740
13,392
39,861
167,767
352
1345
917
3057
Number of genes with
phenotype annotations
Number of phenotype
annotations for genes
Number of genes with
disease annotations
Number of disease
annotations for genes
Number of QTL with
phenotype annotations
Number of QTL with
disease annotations
Number of strains with
phenotype annotations
201
1723
388
2303
429
2218
636
8867
695
1467
568
1426
201
757
Number of strains with
disease annotations
66
588
Disease Portals
In response to the research interests of the rat community, in 2008 RGD released
the Cancer Portal highlighting genetic and genomic elements related to Breast Cancer and
Urogenital Cancers. RGD has three other portals as well: Cardiovascular Diseases,
Neurological Diseases, and Obesity/Metabolic Syndrome.
Pathway Data
Development of pathway data continues with the release of interactive diagrams.
These diagrams provide a description of the pathway as well as an illustration linked to
gene reports and to PubChem reports for other molecules. In addition there are links to
references, and ontology reports. The diagrams also provide links to interacting
pathways. There currently are 23 diagrams available. RGD currently has 1345 genes
annotated with pathway information.
New Tools and Components
In the past year, RGD has released a new version of its Genome Viewer with new
zoom and data export functions. Users may also include additional data through
subsequent searches as well as add and remove individual objects. In addition, links to
GBrowse allow the user to add data tracks and view additional details. A new Version of
GBrowse includes mouse and human synteny tracks as well as SNPs from dbSNP and
Ensembl. New tracks for Copy Number Variants, miRNAs, and contigs were also added.
A user can also mouse over any element for a pop up balloons with description details
and links to reports. Enhanced zoom and drag and drop functions also add functionality.
Usage Statistics
Use of RGD continues to rise with more than 1.05 million page views involving
over 122,000 visits by 72,869 visitors in the past year. These users accessed RGD from
161 countries. A typical user visits more than 8 pages on RGD during a single visit. The
components most often accessed are illustrated in the table below for the four quarters of
2008.