|
|
| October 29, 2009: MGI announces the following enhancements for the 4.31 release. |
| |
| Cre Recombinase Portal |
- MGI has released a Cre Recombinase Data Portal that specifically addresses the need to access cre expression and specificity data (www.creportal.org). Through this portal, users can access information about all existing cre transgenes and knock-ins. Data include molecular description of the cre transgene or knock-in, the driver / promoter used, inducibility information, publications, and availability of cre mice through the IMSR. Detailed data, including annotated images showing cre activity / expression for the tissues analyzed are being added as available. Access to phenotypes displayed by cre-deleted mice is provided via integration with MGI's phenotype data.
- Currently, there are over 1,040 recombinase-containing transgenes or knock-in alleles cataloged.
- To search for recombinase-containing transgenes or knock-in alleles:
- Select an anatomical system from the search for Recombinase specificity in: pick-list: the results will list those transgenes and knock-in alleles where cre specificity/expression is found in the anatomical location selected.
- Select a driver from the Recombinase driven by: pick list: the results will display transgenes and knock-in alleles utilizing the chosen driver.
- To find a mouse carrying a cre recombinase transgene or knock-in:
- On the Summary table that is returned from a search (as described above), scroll right to the IMSR column. A numeral in this column indicates how many matching items there are in the International Mouse Strain Resource. Click the numeral link to bring up an IMSR summary table of strains expressing cre recombinase. The IMSR provides links to Repositories holding these mice and to MGI phenotype data for cre-mated mice.
- To retrieve a table of all cre-containing transgenes and knock-in alleles:
- We provide
reports of all recombinase-containing transgenes and knock-ins cataloged, regardless of the anatomical system in which they show specificity or are expressed and regardless of the driver used.
- Related searches:
- Use the Phenotypes, Alleles, & Disease Models Query Form to find recombinase-containing transgene or knock-in alleles or to find flox- or frt-containing alleles. Here you will find allele-specific data and phenotypes resulting from crosses with cre-containing transgenes and alleles.
- Use the Gene Expression Data Query Form to find endogenous gene expression results for cre-containing knock-ins.
- Transgenic allele nomenclature:
|
| |
| Submitting Data to MGI |
- MGI 4.31 also features a new data submission form for submitting new allele/mutants, registering a mouse strain name, or submitting phenotype data. In addition, data file downloads are encouraged.
- The new submission form offers more flexible information management and easy access to examples and data checks, as well as ready access to personal help with the process.
|
|
|
August 19, 2009: MGI announces the following enhancements for 4.3: |
- This release adds over 500,000 mouse cell line and gene trap sequences for gene traps in the NCBI Genome Survey Sequences Database (dbGSS), including those from the International Gene Trap Consortium (IGTC), and from Lexicon Genetics.
- MGI Gene-trapped Allele Detail pages provide:
- a genome browser view of the gene trap insertion site.
- sequence tag information, including genome coordinates.
- cell line IDs from organizations supplying gene trap sequence data to dbGSS.
- information about the parent stem cell line and the gene trap vector used to produce each mutant.
- identification of any mouse models with phenotypic similarity to human diseases associated with the allele.
- links to the International Mouse Strain Resource (IMSR) for access to available mouse strains and cell lines.
- information about whether a mouse has been produced for the gene trap mutant cell line.
- allele nomenclature.
- As examples, see:
- How MGI associates gene traps to genes
- The MGI gene trap load associates gene traps to genes using genome-wide sequence alignments (BLAT) with gene trap sequence tags.
- We compute the single point coordinate best approximating the gene trap vector insertion site for each sequence tag from the resultant sequence tag genome coordinates.
- We compare the gene trap sequence tag coordinates/strands to MGI gene coordinates/strands to detect trapped genes and to establish allele-to-gene relationships.
- A gene trap allele-to-gene association is made only if the gene trap insertion "traps" the gene.
- MGI updates gene-trap-to-gene associations weekly.
- Associations that MGI does not make
- MGI does not establish gene-trap-to-gene associations:
- where sequence tags for a gene trap allele overlap multiple genes in the trapped gene orientation; where tags overlap one or more genes in reverse orientation; or where they overlap no known genes using current gene model coordinates.
- where gene trap sequence tags for an allele do not align with the reference mouse genome, or align equally well to multiple locations.
- for mixed cell lines, characterized by multiple sequence tags for the same cell line and good alignments to different locations in the genome.
- See Why aren't all gene traps associated with a gene? for additional details.
- Gene Trap Integration and Curation at MGI
-
- MGI regularly integrates dbGSS sequence tag data with curated gene trap information.
- On-going curatorial activity associates published mouse phenotype data, derived from mice produced from gene trap cell lines, with allele records generated from the data.
- Finding these associations in MGI
-
- For more information, see:
-
|
|
|
March 26, 2009: MGI announces the following enhancements for release 4.21
|
- The MGI Batch Query now provides the option to return expression data from MGI. Enter a list of genes and click Gene Expression (under Additional Information).
- The MGI Batch Query now accepts microarray probeset IDs from two Affymetrix Platforms (Mouse Gene 1.0 ST Array and Mouse Genome 430A 2.0 Array). As an example, you could enter a list of up- or down-regulated probes from a microarray experiment and get different types of MGI data for these genes (Gene Ontology, Phenotypes, Gene Expression, and so on).
- Each MGI gene detail page now has a link to all microarray probe sets (from the two Affymetrix platforms) for that gene. As an example, see Fgf4.
- If you want to download all microarray probeset to gene associations, see
MGI Data and Statistical Reports.
- There is a new evidence code under Gene Ontology (GO) Classifications: EXP, Inferred from experiment.
- MGI gene detail pages now also link to:
- GO Consortium Reference Genome Project (from Gene Ontology (GO) Classifications) for any genes included in this project
- MouseFunc, a functional prediction resource (from Gene Ontology (GO) classifications)
- International Knockout Mouse Consortium (IKMC)
Status (indicates a gene's status in gene targeting pipelines (under Other database links).
- An MGI Tutorial is now available from Open Helix.
- The remainder of the release comprises performance improvements and upgrades.
|
|
|
January 12, 2009: MGI Quick Search enhanced for release 4.2
|
- The Quick Search tool provides a swift and powerful overview of MGI data. You can:
- Query for gene symbols (or names, synonyms, orthologs), strings of text (e.g., key words from MGI vocabularies), or accession IDs, singly or in combination, in the Quick Search box.
- View the best matches, separated into Genome Features, Vocabulary Terms, and Other Results by ID (e.g., references, sequences).
- Follow links to deeper layers of MGI data such as genes/markers, additional vocabularies, expression results, many IDs.
- Forward results to the MGI Batch Query tool (and access additional MGI data such as genome location, vocabularies, gene attributes).
- Iterate your query to find ever more relevant results.
- Search MGI using Google.
|
|
