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Human and Mouse Orthologous Transcript Nomenclature Meeting April 22, 2005

The Jackson Laboratory. Human and Mouse Orthologous Transcript Nomenclature Meeting April 22, 2005. Lois J. Maltais Mouse Genome Informatics (MGI) The Jackson Laboratory Bar Harbor, ME. Mouse Genomic Nomenclature Committee (MGNC )

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Human and Mouse Orthologous Transcript Nomenclature Meeting April 22, 2005

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  1. The Jackson Laboratory Human and Mouse Orthologous Transcript Nomenclature MeetingApril 22, 2005 Lois J. Maltais Mouse Genome Informatics (MGI) The Jackson Laboratory Bar Harbor, ME

  2. Mouse Genomic Nomenclature Committee (MGNC) Standardized Genetic Nomenclature of Mice to implement nomenclature standards for mice. Lois J. Maltais Dr. Janan Eppig Dr. Judith Blake Lindsay McClellan Monica McAndrews-Hill E-mail: nomen@informatics.jax.org Voice: 207-288-6429 Fax: 207-288-6132 MGNC International Committee on Standardized Genetic Nomenclature for Mice

  3. The Jackson Laboratory Education Research Resources

  4. Genotype Expression Phenotype Mouse Genome Database (MGD) Gene Expression Database (GXD) Mouse Genome Sequencing Project (MGS) Mouse Tumor Biology Database (MTB) Objective: Facilitate the use of the mouse as a model for human biology by furthering our understanding of the relationship between genotype and phenotype. www.informatics.jax.org

  5. Mapping data Strains Polymorphisms Sequence Mutant alleles and Phenotypes Tumor data

  6. Sources of New Genes and Loci For MGI Mutagenesis NCBI/Entrez-Gene TIGR/DOTS MGC/RIKEN HGNC/ Gene Family/ Community Literature ESTs Literature MGSC Evaluation of Equivalency/Novelty/Redundancy MGI QC !

  7. Curation of Sequence-to-Gene Associations is Key to the Integration of Sequence and Biology MGI Entrez-Gene RefSeq RIKEN MGC Nucleotide Sequences • Nomenclature • Chromosomal location • Orthology • Expression • Alleles • Mutant phenotypes • Function of gene products • Experimental data • Sequence • Literature SwissProt Protein Sequences “Gene” Electronic Transcripts Computational Genome Annotation Pipelines TIGR/DOTS

  8. General MGI Statisticsas of 1 April, 2005 • Number of Genes: 31187 • Number of Genes with Sequence: 27758 • Number of Genes Mapped: 30376 • Number of Orthologies Mouse/Human: 14935 • Number of Orthologies Mouse/Rat: 12706 • Number of References: 91544

  9. Phigs

  10. Nomenclature Quality Control Reports Nomenclature 1. Nomenclature Symbols Broadcast Within Last 3 Days 2. Nomenclature In Progress Symbols 3. Nomenclature Reserved 4. MGI Symbols differing from Human Ortholog Symbols, excludes RIKEN (#1) 5. MGI Symbols differing from Human Ortholog Symbols, excludes RIKEN (#2) 6. MGI Symbols differing from Human Ortholog Symbols, RIKEN only (#1) 7. MGI Symbols differing from Human Ortholog Symbols, RIKEN only (#2) 8. Withdrawn Markers 9. Interim Markers (sorted by Date) 10. EST IDs and Gm Markers as Synonyms 11. MGI Markers with Uninformative Nomenclature #1 12. Human/Mouse Orthologies involving RIKEN Symbols 13. Synonyms that require proper J number assignment 14. Synonyms that need to be verified

  11. Quality Control ReportRik symbols with human orthologous information

  12. FANTOM 3RIKEN - MGI 30,000 F3 clones (new) • 25,000 clustered into existing new genes • 5,000 singletons (Waiting in “wings” till publication. Reanalyze) Mapped library to Anatomical Dictionary Assigned GO annotations to clones

  13. Thank you!

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