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The Jackson Laboratory Mouse Genome Informatics Site: Version 2.3.2 Yeast Yeast 2000; 17: 134±145. Website Review The Jackson Laboratory Mouse Genome Informatics Site: Version 2.3.2 http://www.informatics.jax.org/ Site authors: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, Maine. Project PI: Janan Eppig. All screen views from the website are reproduced with the kind permission of Janan Eppig. Jo Wixon Managing EditorÐSchool of Biological Sciences, University of Manchester, Manchester, M13 9PT, UK Site structure user to ®nd the right page to answer his/her query and I have followed this structure for the site guide. The main page is broken down into three sections: Most of the links go through to a page with a list of services, headed by the same title. Each title forms a Searches, data and reports searches of subsections link to the relevant section of the site overview; this of the databases): gives information about the available data, and an $ Genetic and phenotypic data. explanation of what the searches offered on the $ Mapping and marker data. page are designed to do. In some cases, the titles $ Strains and polymorphisms. link to instructions on how to use the searches and $ Expression data some entries include ®gures of tools. Above these titles are links to each of the results from published work). other search topic pages; these allow more rapid $ Mammalian homology data includes Oxford movement around the site. Between these links and grids and comparative maps). the title, on every page, is a pull-down menu, for $ Database reports view the data as lists, as an those who wish to go directly to a search form. This alternative to searching). includes a link to the `quick [search] forms', which $ Chromosome committee reports. have fewer ®elds to be completed. $ Contributed datasets these have not been inte- grated into the databases). Prototypes services and databases that are still Searches, data and reports under development): $ BLAST service. This section provides searches of subsections of the $ Mouse Tumour Biology database MTB; Bult vast collection of mouse data held in the Mouse et al., [2000]). Genome Database MGD; Blake et al., [1999]), the $ Rat genome data. Mouse Genome Sequence Database MGS) and the Other MGI resources: Gene Expression Database GXD; Ringwald et al., $ Advice on nomenclature. [1999]) at the Jackson Laboratory. In addition to $ Data submission guidelines. the links described below, there is a small query box $ User support page. for a quick search of the genes catalogue. $ E-mail-based discussion lists users can subscribe to these). Genetic and phenotypic data Searches Site guide The `Genes, Markers and Phenotypes' link leads to a query form that allows the user to search by locus The main page of Mouse Genome Informatics symbol, name, map position, and many other MGI) is a list of links to subpages Figure 1). characteristics. Clicking on `Combined Mouse/ This topic-based breakdown of the data helps the Human Phenotypes' leads to a form for a simulta- Copyright # 2000 John Wiley & Sons, Ltd. Website Review 135 Figure 1. The main page of the Mouse Genome Informatics website neous keyword search of the Mouse Locus Catalo- homology, polymorphisms, and gene expression gue MLC) and Online Mendelian Inheritance in patterns. There are also some general statistics and Man OMIM). Users can also search for poly- links to nomenclature information. The markers are morphisms by type PCR or RFLP), locus symbol, sorted by name or chromosome and the last map position or strain. A search for the character- month's updates are available. The mouse±human istics of inbred strains in M. Festing's Listing of homology and mouse±rat homology results are Inbred Strains of Mice and Rats is also offered. The sorted by chromosome or gene symbol in each `Quick Forms' link `does exactly what it says on the organism. tin' and leads to a broken down listing of all possible searches, each of which leads through to a Data submission tools and guidelines simple form with fewer criteria, allowing a more The `Mouse Nomenclature Guidelines and Locus rapid search. Symbol Registry' link is intended to be a guide for users who wish to name and register a gene or Reports locus. It gives details of the nomenclature commit- The `Chromosome Committee Reports' link leads tee and their recommendations and gives links to to an archive of the reports of each chromosome databases so that users can check that their chosen committee, for the current year and previous years name is not already in use. The second link, going back to 1995. The `database reports' link `Submitting Mouse Genome Data', is very self- leads to MGI data on genetic markers, mammalian explanatory. It contains guidelines for those who Copyright # 2000 John Wiley & Sons, Ltd. Yeast 2000; 17: 134±145. 136 Website Review wish to submit mouse data to MGD. There are chromosome number on the mouse axis links to the detailed instructions and examples of each section entire comparative map of that mouse chromosome of the forms. with the second chosen organism. Another service offered in this section of the site is to build a Molecular probes and segments `comparative map'. The user can specify the format of the map, the source of information for the map Searches and the chromosome or region of interest in the This page links to a search of all the information mouse genome. Next, the types of markers to be held on probes and segments in the mouse maps. included in the map are selected, and the second This search can yield information about the source genome is chosen from a list. There is even an of a probe, to which loci it hybridized and the option to add a marker/s that the user has mapped sequence of the probe if known. There is also a link independently. Once the form has been completed, to the `Quick [query] forms'. the map is obtained by clicking the `retrieve' button; an example of a short-range map is shown in Reports Figure 3. Whilst this makes an excellent ®rst port of There is a link to the probes section of the `database call for researchers wanting to identify regions of reports' pages described in the `Genetic and synteny between the mouse genome and another Phenotypic Data' section. mammalian genome, it does only provide coarse Mammalian homology and comparative maps data, i.e. mapped orthologues, rather than taking advantage of the sequencing data which is available. This page has links to services which access This section also contains a link to the quick homology information for mouse, human and 17 forms, described previously. other mammalian species, most of which has been extracted from published scienti®c literature. In Reports particular, the Mammalian Homology search and The `Mouse/Drosophila Homologies' link leads to a the Oxford grid tool will be of great interest to any table of homologous genes found in both the mouse readers working on mammalian genomes. Since there and ¯y genomes, compiled by Michael Ashburner. is no obligation to use the mouse as one of the species, There is also a link to the Mammalian Homology any pair from the 17 species can be compared. section of the database reports page. Searches Homology criteria The `Mammalian Homology' search offers several There are links to the report of the 1995 HUGO options, from obtaining all the homologous genes Human Genome Organization) committee on between two species, through specifying a chromo- comparative mapping and to the homology criteria some or chromosome region, to specifying the name as de®ned by this committee) that are used by of a particular marker gene) or the author of a MGD to describe mammalian homologues. paper. All of the titles of the search criteria in the form link to an explanation of how to enter a Maps and mapping data search term. The `Oxford grid' tool will produce a plot of the The title of this page links to detailed guidelines for homologous loci between two genomes from a using the searches offered on the page. choice of seven. The x and y axes of the plot are the chromosomes of the two species, such that there Searches is a cell for each possible combination of chromo- The `Mapping Data' search allows users to retrieve somes Figure 2). The number of matches for that mapping data on any chosen marker or markers. pair of chromosomes appears in the box and colour The type of experiment used can be speci®ed, e.g. coding is given to aid the user to spot chromosomes FISH, or all of the data available can be retrieved. with many genes that are homologues. Clicking on Other criteria can be used for this search, such as a box from the grid leads to a table of all the chromosome and experiment type, to yield all of the homologous loci on that pair chromosomes. If mapping data produced for chromosome 11 using mouse is one of the chosen organisms, then each somatic cell hybrids HYBRID), for example. Other Copyright # 2000 John Wiley & Sons, Ltd. Yeast 2000; 17: 134±145. Website Review 137 Figure 2. An Oxford Grid comparing the mouse and human genomes. The chromosomes from the two species form the axes of the plot, and the numbers in each cell indicate how many homologues there are on each pair of chromosomes. The cells are colour coded to give a quick indication of the number of homologues. Grey=1 Blue=2±10 Green=11±25 Orange=26±50 Yellow=50+. This grid represents 4232 homologies, 3040 of which have been mapped in both species ®elds include author name and MEDLINE Acces- of the progeny.
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