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Phenotype mutant allele definitions QTL strain characteristics phenotype vocabularies

QTL Annotation in MGI Susan M Bello, Ira Lu, Cynthia L Smith, Janan T Eppig, and the Mouse Genome Informatics Group. Sequences & Maps sequence representation C57BL/6J genomic sequence SNPs and strain variants adding biological context to computational gene models. Genes & Gene Products

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Phenotype mutant allele definitions QTL strain characteristics phenotype vocabularies

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  1. QTL Annotation in MGISusan M Bello, Ira Lu, Cynthia L Smith, Janan T Eppig, and the Mouse Genome Informatics Group

  2. Sequences & Maps • sequence representation • C57BL/6J genomic sequence • SNPs and strain variants • adding biological context to computational gene models • Genes & Gene Products • nomenclature • gene characterization • transcripts, proteins, gene products • functional annotation • orthologs & paralogs • Gene Expression • mouse anatomy • time, tissue, level of expression • range of assays & results • emphasis on embryonic stages • Tumor Biology • tumor classifications & descriptions • strain incidence • histopathology images • tumor genetics Overview of Mouse Genome Informatics (MGI) • Phenotype • mutant allele definitions • QTL • strain characteristics • phenotype vocabularies • disease models (human) • comparative phenotypes

  3. QTL Annotation: Present and Future • Current format • Problems with using the Mammalian Phenotype (MP) ontology to annotate QTL • Display of mapping information • Display of variant and parent strain phenotypes

  4. Current QTL Display

  5. Current QTL display + +

  6. Mammalian Trait Ontology • Purpose: annotate QTL and strains • Adapted from the MP Ontology • Absolute traits rather than relative phenotypes • ~3700 trait terms compared to ~4800 phenotype terms

  7. Mammalian Trait Ontology Mammalian Phenotype Ontology

  8. Mammalian Trait Ontology

  9. Proposed QTL Display Genome coordinates: 132851306-135646474 (MGI Mouse GBrowse)

  10. Current QTL display in MGI

  11. GO Alexander D. Diehl Harold J. Drabkin David P.Hill Dmitry Sitnikov Software Engineering Jon S. Beal Lori E. Corbani Sharon L. Giannatto Diane J. Dahmen Mary Dolan Richard M. Balderelli David B. Miers Matt Vincent Peter Frost Michael B. Walker GXD Terry E. Hayamizu Ingeborg J. McCright Constance M. Smith Jacqueline H. Finger MGI Staff PI Janan T. Eppig Judith A. Blake Carol J. Bult Martin Ringwald James A. Kadin Joel E. Richardson Phenotypes Donna L. Burkart Anna Anagostopoulos Ira Lu Cynthia L. Smith Susan M. Bello Megan Updegraff Howard Dene Beverly Richards-Smith Linda L. Washburn Randal Babiuk Hiroaki Onda Monika Tomczuk Software QA Mark Airey Jeffrey W. Campbell Jill R. Lewis MTB Debra M. Krupke Dale A. Begley SysAdmin Matthew J. Baya Mike J. McCrossin Leslie A. Miller Iry T. Witham Sequences and Maps Dirck W. Bradt Yunxia Zhu Kenneth Frazer Deborah J. Reed Robert Sinclair T.B.K. Reddy Administrative Deborah E. Geel Janice E. Ormsby User Support David R. Shaw Paul Szauter Susan McClatchy Genes/Gene Products Nancy E. Butler Lois J. Maltais Monica McAndrews-Hill Li Ni Funding NHGRI (HG000330, HG002273) NIH/NICHD (HD033745) NCI (CA089713)

  12. disease phenotype 1 phenotype 2 trait A trait B trait C trait D

  13. Mammalian Trait Ontology vs Mammalian Phenotype Ontology

  14. Mammalian Phenotype Ontology

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