Mouse Genome Informatics: Other Contributed Data Sets and Tools

These data sets have been contributed to MGI by the authors. Currently they are not directly incorporated into the relational database. They are provided here as text or Excel files for the scientific community to view or download. We encourage contributions of such specialized important data sets that may be outside the structured information maintained in MGI as a vehicle for community collaborations. For data submission guidelines, see http://www.informatics.jax.org/submit.shtml or send email to User Support.

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Table of Contents
  1. ENU Incidental mutation data files
  2. The T31 RH Mapping Panel for the Laboratory Mouse and the Associated MGI Markers
  3. Major Histocompatibility Complex H2 Haplotypes
  4. The Genealogy Chart of Inbred Strains
  5. Polymorphisms in Microsatellite Markers for 129X1/SvJ vs Other Inbred Strains
  6. RI Strain Distribution Patterns (MGI)
  7. RI Strain Distribution Patterns for AXB and BXA (Paigen)
  8. RI Strain Distribution Patterns for AXB and BXA (Prows)
  9. 2-Cell Embryo Gene List
  10. MIT STS Marker Data Files
  11. ES cell in situ hybridization data (M.S. Ko)
  12. FANTOM Consortium Gene Ontology Annotations
  13. Exome Sequencing data used to identify candidate genes modifying the Parkinson's phenotype of the Park7 gene
  14. Polymorphisms for Microsatellite Markers in 10 Inbred Strains
  15. MGI Curated STS Markers
  1. ENU Incidental mutation data files
    Data sets are provided by ENU mutagenesis centers that list putative mutations discovered by sequencing genomes of mutagenized mice. These may be present in stocks generated by these projects. Files are available as MS-Excel spreadsheets.

  2. The T31 RH Mapping Panel for the Laboratory Mouse and the Associated MGI Markers
    Reference: J:68900, The Jackson Laboratory Mouse Radiation Hybrid Database, Mouse T31 Radiation Hybrid Data Load.

  3. Major Histocompatibility Complex H2 Haplotypes
    Reference: Appendix F of The Jackson Laboratory Handbook on Genetically Standardized Mice, HTML version by MGI Staff.

  4. The Genealogy Chart of Inbred Strains
    Reference: J:59229, Beck JA, Nat Genet 2000;24():23-25.

  5. Polymorphisms in Microsatellite Markers for 129X1/SvJ vs Other Inbred Strains
    Reference: J:43843, Markel P; Shu P; Ebeling C; Carlson GA; Nagle DL; Smutko JS; Moore KJ, Theoretical and empirical issues for marker-assisted breeding of congenic mouse strains., Nat Genet 1997 Nov; 17(3):280-4

  6. RI Strain Distribution Patterns

  7. RI Strain Distribution Patterns for AXB and BXA
    Specially curated data sets available as MS-Excel Spreadsheets, by Chromosome.

    Reference: J:45463, Sampson ST; Higgins DC; Elliot RW; Taylor BA; Lueders KK; Koza RA; Paigen B, An edited linkage map for the AXB and BXA recombinant inbred mouse., Mamm Genome 1998 SEP; 9(9):688-694

  8. RI Strain Distribution Patterns for AXB and BXA
    Reference: Prows, D.R. and Horner, M.L. Parental genetic contributions in the AXB and BXA recombinant inbred mouse strains. Mammalian Genome 13: 127-133 (2002)

  9. 2-Cell Embryo Gene List
    Reference: Evsikov AV, de Vries WN, Peaston AE, Radford EE, Fancher KS, Chen FH, Blake JA, Bult CJ, Latham KE, Solter D, Knowles BB. 2004. Systems biology of the 2-cell mouse embryo. Cytogenet Genome Res. 105(2-4):240-50.

  10. MIT STS Marker Data Files With Release Data
    Reference: J:34136, Whitehead Institute/MIT, Center for Genome Research, Database Release 1999;()

  11. ES cell in situ hybridization data
    Reference: J:129777, Carter MG; Stagg CA; Falco G; Yoshikawa T; Bassey UC; Aiba K; Sharova LV; Shaik N; Ko MS, An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells., Gene Expr Patterns 2008 8(3):181-98.

  12. FANTOM Consortium Gene Ontology AnnotationS
    The file below contains Gene Ontology (GO) annotations contributed by the FANTOM Consortium and RIKEN Genome Exploration Research Group, as described in the following publications:

    Okazaki Y, et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-73.

    Carninci P, et al. 2006. The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63.

    The file is in standard GO gene association file format (see: http://www.geneontology.org/GO.format.annotation.shtml for details).

  13. Exome Sequencing data used to identify candidate genes modifying the Parkinson's phenotype of the Park7 gene
    Reference: J:186833, Rousseaux, MWC et al Progressive dopaminergic cell loss with unilateral-to-bilateral progression in a genetic model of Parkinson's disease, PNAS Sept, 2012

  14. Polymorphisms for Microsatellite Markers in 10 Inbred Strains
    Reference: Gurumurthy CB; Joshi PS; Kurz S; Ohtsuka M; Quadros RM; Harms DW; Lloyd K. Validation of Simple Sequence Length Polymorphism (SSLP) regions of commonly used mouse strains for marker assisted speed congenics screening. International Journal Of Genomics. 2015.

  15. MGI Curated STS Markers
    MGI-curated relationships between STS markers (STS) and genome features (GF) [genes, pseudogenes, other genome features, etc.].