Using the Gene Expression Batch Search
Using the Gene Expression Batch Search
This help document answers the following questions about the Using the Gene Expression Batch Search:
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).
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.
This is included as a tab on the Gene Expression Data Search or as a Forward feature located on the Genome Features tab of the Quick Search Results summary.
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.
MGI:96677 Trp53 Pax-6 P53 16590 ENSMUSG00000005672 OTTMUSG00000015949 247073 MI0000248 10379153
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 type Representative example MGI Gene/Marker ID MGI:96677 Current Symbols Only Trp53
Pax6
D11Mit10All Symbols/Synonyms/Orthologs
(includes both current and old symbols)Pax6
Pax-6
Trp53
P53Entrez Gene ID 16590 Ensembl ID ENSMUSG00000028530 UniGene ID 247073 MiRBase ID MI0000248 GenBank/RefSeq ID* NM_001122899
AK033644
NP_666257UniProt ID P48356
A2AKJ2GO (Gene Ontology) GO:0019221 RefSNP ID rs3021544 Affy Probeset ID 10379153 * GenBank IDs are for nucleotide sequences only. RefSeq IDs are for either nucleotide or protein sequences.
Input identifier type Representative example EC
(Enzyme Commission)2.7.10.1 Homologene 20151 PDB
(Protein Data Bank)1HU8 Consensus CDS CCDS16941.1 Protein Ontology PR:000004803
Yes, you can import a column from a text file. In the Use IDs from a File section of the form:
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. There is a 5000 gene limit for this query.
You may wish to select a single input type from the Type list when you want the Batch Query to return:
Yes, you can.
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.
See: How do I interpret the query results summary pages?
Yes. The Genes and Assay Results tabs provide export options.
Yes. Under the Genes tab you have the option of exporting your results as a text file or sending the list of genes to the MGI Batch Query or MouseMine.
See also Using the MGI Batch Query.
Yes. Click on the RNA Seq ► Heat Map button above the table of results in the Assay results tab. A browser window will open, displaying your selected data in Morpheus, a heat map visualization and analysis tool created at the Broad Institute. All the processing of the data you do will be done on your computer, not on MGI's (or the Broad's) servers. Heat map images and files can be saved using Morpheus.