Using the Gene Expression Batch Search
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This help document answers the following questions about the Using the Gene Expression Batch Search:

What is the purpose of the Gene Expression Database?

The Gene Expression Database (GXD) is designed to integrate many different types of endogenous gene expression data from the mouse in formats appropriate for comprehensive analysis. Query results, such as the developmental stage and tissue of expression (or non-expression), the genetic origin of the sample, and the numbers and sizes of detected bands, are described together with the molecular probe, the expression assay type, and the experimental conditions used. Expression patterns are described using an extensive, hierarchical dictionary of standardized anatomical terms, making it possible to record expression results from assays with differing spatial resolution in a consistent and integrated manner and to analyze expression patterns at differing levels of detail. Whenever possible, text annotations are complemented by digitized images of the original expression data.

To learn more about GXD and how we acquire data, please see About the Gene Expression Database (GXD).

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What can I use this query form to find?

The Gene Expression Data Query form Batch Search tab allows you to retrieve expression data with a list of genes or IDs associated with genes. All Gene Expression Data searches return a tissue-by-gene matrix view as part of its multi-tabbed data summary. This view enables a comparison of expression patterns between genes. Data filters found on the summary pages can be used to further refine search results.

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What are the accepted input identifier (ID) types?

For a given query, your list can be either mixed or all of the same type. You can also enter (mouse) gene symbols, synonyms, or orthologs.


The following are representative examples for each type listed on the pulldown menu:
Input identifier typeRepresentative example
MGI Gene/Marker IDMGI:96677
Current Symbols OnlyTrp53
Pax6
D11Mit10
All Symbols/Synonyms/Orthologs
(includes both current and old symbols)
Pax6
Pax-6
Trp53
P53
Entrez Gene ID16590
Ensembl ID ENSMUSG00000028530
VEGA IDOTTMUSG00000015949
UniGene ID247073
MiRBase IDMI0000248
GenBank/RefSeq ID*NM_001122899
AK033644
NP_666257
UniProt IDP48356
A2AKJ2
GO (Gene Ontology)GO:0019221
RefSNP IDrs3021544
Affy Probeset ID10379153
 
*    GenBank IDs are for nucleotide sequences only. RefSeq IDs are for either nucleotide or protein sequences.
The following are additional types (not listed on the pulldown menu), followed by examples, of other types of IDs that the Batch Query recognizes:
Input identifier typeRepresentative example
EC
(Enzyme Commission)
2.7.10.1
Homologene20151
PDB
(Protein Data Bank)
1HU8
Consensus CDSCCDS16941.1
Protein OntologyPR:000004803

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Can I upload a particular column of IDs/Symbols from a file?

Yes, you can import a column from a text file. In the Use IDs from a File section of the form:

  1. Select your file type: tab-delimited or comma separated.
  2. Click the Choose File button to browse for your file.
  3. In the ID/Symbols column: field, type the column number that you wish to import.

Note: To import a column of symbols or IDs from a spreadsheet, first export the file as text or CSV (Comma Separated Values) and then import the column or copy and paste a column directly from the spreadsheet.

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When would I constrain my search to a single input type?

You may wish to select a single input type from the Type list when you want the Batch Query to return:

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Can I edit my original options and requery?

Yes, you can.

Notes:

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How do I filter my results?

You can filter results by Anatomical System, Assay Type, Theiler Stage, or by whether expression was Detected or whether the data are for Wild type or mutant specimens. In the banner above your results, after Filter expression data by: click the desired box. This will reduce your results to only those containing the checked items. The filters are applied across all data tabs and to any file you export. Note: Filtering out mutants will retain heterozygous in situ knock-in mutants.

Both Matrix tabs offer easy filtering by tissue. The Tissue x Stage Matrix also offers filtering by developmental stage/age and the Tissue x Gene Matrix permits filtering by gene symbol. Check the rows or columns you wish to retain and then click the Filter () button in the grid to apply the filters. These filters are also applied to all tabs.

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How do I interpret the query results summary pages?

See: How do I interpret the query results summary pages?

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Can I get my results as tab-delimited text or spreadsheet files?

Yes. The Genes and Assay Results tabs provide export options. In your search results, click on the Text File or Excel File icon. Your web browser will download a file of the results.

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Can I send the results of my search to the MGI Batch Query or MouseMine?

Yes. Under the Genes tab you have the option of exporting your results as a text file, spreadsheet file or sending the list of genes to the MGI Batch Query or MouseMine.

See also Using the MGI Batch Query.

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