1 / 17

Mouse Anatomy Ontologies and GXD

Terry F. Hayamizu Mouse Genome Informatics, The Jackson Laboratory . Mouse Anatomy Ontologies and GXD. Gene Expression Database (GXD) . Currently, GXD includes:

gauri
Download Presentation

Mouse Anatomy Ontologies and GXD

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Terry F. Hayamizu Mouse Genome Informatics, The Jackson Laboratory Mouse Anatomy Ontologies and GXD

  2. Gene Expression Database (GXD)

  3. Currently, GXD includes: • a comprehensive literature index for mouse gene expression, with a primary emphasis on endogenous expression during embryonic development, covering >14,000 genes studied in >18,500 primary references • detailed experimental data for >12,700 mouse genes in >50,000 expression assays from ~5000 references, including data for >1,500 mouse mutants, as well as >200,000 images associated with expression data • over 1 million gene expression results annotated to specific mouse anatomy terms

  4. stage-dependent DAGs stage-independent DAG Stage i s S t u v T U V x w X Y Stage j W s EMAPA u v x y EMAP

  5. anatomy ontology for the postnatal mouse anatomy ontology for mouse development developed by EMAP developed by GXD

  6. Represent develops-from relationships TS X “develops-from” relationships TS Y EMAP / EMAPA TS 28 MA

  7. GENE EXPRESSION GENOTYPE PHENOTYPE DISEASE MODELS GENETICS

  8. Gene Expression Phenotype Anatomy Disease Biological Process Pathological Process

  9. Mammalian Phenotype ontology Gene Expression Database Adult Mouse Anatomy NCI Thesaurus Gene Ontology Pathbase

  10. Gene Expression Gene Expression Phenotype Phenotype Biological Process Anatomy Anatomy Disease Biological Process Pathological Process Disease Pathological Process Gene Expression Phenotype Biological Process Anatomy Pathological Process Disease

  11. Anatomical ontologies from other species

  12. Other Mouse Genome Informatics (MGI) resources Mammalian Phenotype Ontology (MP) Gene Ontology (GO) Cell Ontology (CO) Edinburgh Mouse Atlas Project (EMAP) Duncan Davidson Richard Baldock Jonathan Bard Matthew Kaufman Gene Expression Database (GXD) Martin Ringwald Janan Eppig Jim Kadin Joel Richardson Jacqueline Finger Ingeborg McCright Constance Smith Jingxia Xu Acknowledgements GXD is funded by NIH/NICHD grant HD033745

More Related