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Mouse Phenome Databases & Mouse Colony Programs Genome Mixer 1.0 MIT SNP Database Gene Mapping and Gene Manager Data Sets The Portable Dictionary of the Mouse Genome OurPrimers DB MIT Microsatellite Database ONLINE Empty copy (clone) of the Portable Dictionary SNP QTL MAPPER in EXCEL format FullDict.FMP.sit Chromosome Text Files from the Dictionary Need Help? Help with Genome DBs Help with Nervenet Contact Us

Mouse Genome Databases This server provides data extracted and compiled from The 2000-2001 Mouse Chromosome Committee Reports Release 15 of the MIT microsatellite map (Oct 1997) The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001) Map Manager and text format chromosome maps (Apr 2001) Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. All files can be used with Macintosh and Windows operating systems. Mouse Genome Databases Note: To use FileMaker and Excel files listed below you may need to configure your web browser to recognize the appropriate file type. You will also need a copy of FileMaker Pro 3.0 or higher and Excel 98 or higher. When you first open FileMaker Pro databases you will be greeted with the message: "This file was not closed properly. FileMaker is now performing a consistency check." This message is normal. LXS genotype Excel file Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. Fifty records are displayed per page in the "list" format. These data from the MIT-Whitehead SNP release of December 1999. INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): We have merged the original MIT SNPs with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the "in silico" mapping method. Download the Excel file to disk. Contact Rob Williams (rwilliams@uthsc.edu) if you have trouble downloading or interpreting these files. View an example of the Excel spreadsheet near the Nnc1/Thra/Rara loci on Chr 11 (58 cM). Our own analysis does not support the idea that the current set of SNPs will be useful for discovery or confirmation of QTLs. The data themselves are fascinating, but there are on average only two or three distinct SNP haplotypes across any region of the genomes of standard inbred strains. Furthermore, as indicated by Grupe et al., recombination densities of SNP haplotypes are surprisingly low reducing the potential resolution. These two characteristics of SNP maps negate their use to map even Mendelian loci. The apparent success of Grupe et al. in using this approach to confirm QTLs (including two of our own; eye weight and retinal ganglion cell number) is a matter of ongoing debate. In any case, you can look over the complete SNP genotypes files now to judge for yourself. Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler's 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was develped by Elissa Chesler. This updated version (Jan 2002) handles missing data. Download the spreadsheet to disk. Correlation matrix for strains included in the Integrated SNP files. This image is a clipping from the Excel file. The two right-most strains, SPRET/Ei and CAST/Ei, are different species and subspecies, respectively, and both need to be treated with special care in any comparative SNP analysis. Some pairs of substrains are > 98% identical.   MIT SNP Database DOWNLOAD the database in tab-delimited text format. This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. MIT SNP Database (DOWNLOAD the FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. Download this version if you have StuffIt or UnStuffIt. File size = 4846 KB. Updated March 19, 1998. MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB below. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB below. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table below into the database. File size = 231 KB. Updated March 19, 1998.   Chromosome Text Files from the Dictionary Chr 01 Chr 08 Chr 15 Chr 02 Chr 09 Chr 16 Chr 03 Chr 10 Chr 17 Chr 04 Chr 11 Chr 18 Chr 05 Chr 12 Chr 19 Chr 06 Chr 13 Chr X Chr 07 Chr 14 Chr Y All 6,100 MIT loci Unmapped loci Reserved loci Personal loci, R. Williams The table to the left lists data on gene loci for individual chromosomes. Data types in these files are separated by tab characters, and each gene or marker locus is separated by a carriage return. The first record in each file lists the names of the variables. You can import the tab-delimited text files into a word processor, but it will be hard to read (adjusting the separation between tabs and creating a hanging indent will help). The files are easy to handle with spreadsheet or database programs (Excel, Filemaker Pro, etc.). Files are sorted alphabetically by locus symbol. If you import data into a spreadsheet or database, you can easily resort the loci by position (Map_ccr = map position from the 1997-98 Mouse Chromosome Committee Reports; Map_mit = map position from the MIT microsatellite map). To download one of these files, hold down the mouse button over the link until a pop-up menu appears, then select the "Save this Link as..." option in the menu. On a Macintosh, you can also just option-click the link to save the file to disk. Another way of saving the file is to load the file normally and just save it as text from within your web browser. You can open the file that you have downloaded using a spreadsheet or database program. If you import text files into Excel, be sure to import it as a tab-delimied file (select Tab-delimited Options in the Open menu). The text files in this table were extracted from the Portable Dictionary of the Mouse Genome. This dictionary includes data on 21,039 loci (genes and anonymous DNA segments). It contains the following types of information: current symbols, old symbols, names, and aliases three sets of data on the positions of loci from the November 1993 GBASE Locus Map from the 1993 and 1994 Chromosome Committee Reports data from the April 1995 MIT SSLP database release sequence accession numbers associated with gene loci locations of homologous genes in human and 10 other mammalian species recombinant inbred strain data strain distribution data of alleles probe and PCR primer data enzyme commission numbers phenotype codes references (in progress) These files are generally smaller than 500k. They include data from Release 15 of MIT microsatellite loci (Oct 97). Updated by Rob Williams and Alex Williams.