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Mouse Genome Informatics

Curatorial Procedures at Mouse Genome Informatics with an Emphasis on Expression Data Constance M. Smith The Jackson Laboratory Bar Harbor, ME. Genotype. Expression. Phenotype. Objective:

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Mouse Genome Informatics

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  1. Curatorial Procedures at Mouse Genome Informaticswith an Emphasis on Expression DataConstance M. SmithThe Jackson LaboratoryBar Harbor, ME

  2. Genotype Expression Phenotype Objective: Facilitate the use of the mouse as a model for human biology by furthering our understanding of the relationship between genotype and phenotype. Mouse Genome Informatics Mouse Genome Database Gene Expression Database Mouse Genome Sequencing Project Mouse Tumor Biology Database Gene Ontology Consortium www.informatics.jax.org

  3. Gene detail page summarizes information in MGI

  4. Gene Expression Database (GXD) • Most data obtained via manual curation • Emphasis on embryonic expression data • Assay types stored are: • In situ: RNA in situ, immunohistochemistry, reporter gene (knock in) • Gels/blots: RT-PCR, Northerns, Westerns, RNase protection, Nuclease S1 • cDNA source data

  5. Principles guiding curation of expression data • Different types of expression data are integrated • Expression patterns are described using controlled vocabularies • Context is provided by integration with other databases

  6. Literature Curation at MGI

  7. As of 10/23/03: 32,257 records 8,904 references 5,590 genes Up to date Complete from early 1990s to the present

  8. As of 10/23/03: 118,576 results 10,329 assays 2,913 genes

  9. Data entered using customized interface

  10. The Anatomical Dictionary—essential to integration

  11. Allele detail Link to images

  12. Image storage allows users to analyze primary data

  13. Allele detail provides description of phenotype using controlled vocabulary

  14. Gene Gene Function Chromosomal Location Where and When Assay type

  15. Mouse Genome Informatics Staff Principal Investigators Janan Eppig Dale Begley Patricia Grant Richard Baldarelli Judith Blake Dirck Bradt Terry Hayamizu Li Ni Carol Bult Donna Burkart David Hill Dong Qi James Kadin Nancy Butler Debra Krupke Deborah Reed Joel Richardson Rebecca Corey Moyha Lennon-Pierce Robert Sinclair Martin Ringwald Howard Dene Ira Lu Constance Smith John Sundberg Harold Drabkin Cathleen Lutz Cynthia Smith Jacqueline Finger Lois Maltais Benjamin Taylor Kenneth Frazer Ingeborg McCright Pierre VandenBorre Carroll Goldsmith TBK Reddy Linda Washburn Igor Mikaelian Yunxia (Sophia) Zhu John Boddy Diane Dahmen Daniel Modrusan Matthew Baya Mary Dolan Leslie Trombley Jonathan Beal Benjamin King Matthew Vincent Jeffrey Campbell Jill Lewis Michael Walker Lori Corbani Michael McCrossin Joshua Winslow Sharon Cousins David Miers Iry Witham David Garippa David Shaw Paul Szauter Daniel Lawrence Lucette Glass Janice Ormsby Masaaki Furuno Alex Diehl Kirk Barsanti Prita Mani David Walton Peter Frost

  16. Anatomical Dictionary for the adult mouse multiple hierarchies • physiological systems • space / histology • sampling

  17. Anatomical Dictionary for the adult mouse multiple hierarchies • physiological systems • space / histology • sampling Describe and view anatomy from different anatomical, physiological, and disease perspectives • Directed Acyclic Graph • 2405 nodes • 2922 edges

  18. Complete image analysis output Background substraction Normalization Additional Data Transformations

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