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Background

Rat Genome Database an introduction Simon N. Twigger, Ph.D. Bioinformatics Research Center Medical College of Wisconsin, Milwaukee. Background. The Rat is a very good model of Human complex genetic diseases (eg. Hypertension, cancer, diabetes, etc)

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Background

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  1. Rat Genome Databasean introductionSimon N. Twigger, Ph.D.Bioinformatics Research CenterMedical College of Wisconsin, Milwaukee

  2. Background • The Rat is a very good model of Human complex genetic diseases (eg. Hypertension, cancer, diabetes, etc) • Rat is a highly developed physiological model system • Ultimate goal of Rat research is to translate results from Rat to Human RGD Background: • One of 8 NIH funded Model Organism Databases (MOD) • Established in 1999 (grown from 4 people to 20+) • Goal - to facilitate rat research, access to data, in particular mapped phenotypes (QTLs).

  3. Support for Rat Research Various rat strains are used as experimental models of Human disease. Rat studies identify regions associated with disease in Rat. Comparative Genomics allows translation to Mouse and Human

  4. RGD Website

  5. Anatomy of the site SEARCH LIST OF MAJOR OBJECTS HELP PAGE CONTENT: TOOL, WEB PAGE, etc. LINKS, INTERNAL AND EXTERNAL

  6. Anatomy of the site SEARCH LIST OF MAJOR OBJECTS HELP PAGE CONTENT: TOOL, WEB PAGE, etc. LINKS, INTERNAL AND EXTERNAL

  7. Lots of Help

  8. Data is from multiple sources Databases Websites Literature Informatic data mining Regular Journal Screening And Curation Data Sources Internal Data External Data Data Pipeline RGD Database Ongoing Data Curation and QA/QC

  9. Data and Tools QTL Report QTLs SSLPs Genes Maps Strains Sequences Current Tools: Genome Scanner - Genetic Mapping/Genome Scans RHMap Server - Radiation Hybrid Mapping VCMap - Comparative Mapping MetaGene - Gene Prediction Coming Soon: Ontology Browser and searches ACP Haplotyper Blast/Blat

  10. RGD: QTLs Search by Trait QTL report.

  11. RGD: References Reference Report Objects linked to reference Search by Author.

  12. RGD: Genes Gene report provides key information about a gene: Name and aliases, curated homologs, functional annotations, mapping data, external database links and curated references.

  13. RGD Tools Helping researchers access and use the data within RGD

  14. Major Tools • Genome ScannerPolymorphic marker selection • VCMapComparative mapping between Rat, Mouse and Human • MetaGeneGene prediction and visualization tool • RH MapserverMap RH vectors to the genome in silico

  15. Genome Scanner Polymorphic marker identification between two strains Easily select marker set for genome-wide scans for disease association

  16. Genome Scanner results Select one marker Per 10cM bin

  17. Virtual Comparative Maps • Virtual Comparative Map (VC Map) • EST-based comparative mapping algorithm • Uses Rat, Mouse and Human RH maps • Allows location predictions based on synteny (Virtual mapping) • Web/Java maps and reports.

  18. Virtual Comparative Maps

  19. VCMap: Virtual Mapping Within a defined syntenic region the location of homologous markers, previously unmapped in Rat, can be predicted.

  20. Community Resources • Rat Community Forum - online bulletin board • Pied Piper - quarterly newsletter • Rat Strain and Gene nomenclature guides • User support - for RGD tools and general rat genomics/bioinformatics questions • Visiting Scientist program - work with RGD to enhance the resources in a specialized area

  21. Acknowledgements • RGD Admin • Howard Jacob • Simon Twigger • Peter Tonellato • Database and Tool Management • Dean Pasko • Jiali Chen • Chunyu Fan • Lan Zhao • Data Integration and Comparative • Analysis • Susan Bromberg • Chin-Fu Chen • Rajni Nigam • Gopal Gopinathrao • Angela Zuniga-Meyer • Data Exploration and Discovery • Mary Shimoyama • Nataliya Nenasheva • Weiye Wang • Data Mining and Advanced Tool Development • Norie de la Cruz • Jed Mathis • Aubrey Hughes • Wenhua Wu • Genome Annotation • Jeff Nie • Victor Ruotti • System Admin & WebMaster • Yuan Ji • Weihong Jin • ----------- • Mouse Genome Database • Janan Eppig • Lois Maltais • NCBI • Greg Schuler • Donna Maglott • Svetlana Dracheva

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