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Batch Data and Analysis Tools
Batch Queries
Batch Query
Input a list of IDs or gene symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO, expression data).
Gene Expression Batch Search
Input a list of IDs or gene symbols and retrieve associated gene expression assay data. Search results include a tissue-by-gene matrix view to enable the comparison of expression patterns between genes.
Powered by InterMine, MouseMine offers flexible querying, numerous predefined query templates, iterative refinement of results, and linking to other model organism Mines. MouseMine:
  • offers many useful "canned" queries, plus point-and-click query editing
  • supports uploading and manipulating lists of objects
  • allows any query result to be downloaded (text, xml, json) or forwarded to Galaxy
Data Files for Download
Public Reports via FTP
  • Over 75 data files are generated weekly and available for download.
  • See MGI Data and Statistical Reports for the list of reports and their field descriptions.
Tab Delimited Output from our Web Interface
  • User-defined results for references, gene and SNP data are available in tab delimited format.
  • You can modify the output format on the query form from Web to Tab-delimited.
  • Query Forms with the tab-delimited option available are:
FASTA Output from our Web Interface
  • The FASTA format is available on reports where sequences are returned for a specific gene or when querying sequences.
  • Click on the checkboxes next to each sequence to select it for FASTA download and click GO.
  • From a gene detail page, FASTA is available for:
    • Representative genomic, transcript, and polypeptide sequences
    • All mouse sequences
    • Human and rat orthologs
    • Mouse, human, and rat protein sequences for superfamily members
Analysis Tools
These tools are in the development phase and subject to change. Please feel free to use them and send us your comments.
VLAD - Visual Annotation Display
VLAD is a tool for visualizing GO annotations. The annotation data are a subset of those available at the GO web site. You specify an annotation data set and a set of genes, and the tool will produce a graphical summary of the annotations.
GO Slim Chart Tool
This GO_Slim Chart Tool bins the genes in your list according to MGI GO Slim definitions to help you discover what the genes may have in common.
GO Term Mapper
This GO Term Finder tool searches for significant shared GO terms used to describe the genes in your list to help you discover what the genes may have in common.

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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Send questions and comments to User Support.
last database update
MGI 6.09
The Jackson Laboratory