Using the Differential Expression Search
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This help document answers the following questions about the Differential Expression 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 Differential Expression Search is specifically designed to allow you to search for genes expressed in some anatomical structures or developmental stages but not in others. Examples of the questions you can ask are:

See Are there examples of query results? for the form field values for these queries.

If you are interested in doing queries that do not involve comparing the presence and absence of expression in various structures or at various stages, use the Standard Search tab on the Gene Expression Data Search Form.

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How do I use this query form?

To search for detailed data using this query form, enter or select values in one or more of the query form fields described in the following paragraphs. After entering values in the form fields, click Search to submit the query. Click Reset to clear the fields and return any default values.

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What values are acceptable in each of the fields?

Anatomical Structure | Developmental Stage | Structure & Stage
This form lets you query for genes expressed in some anatomical structures and/or developmental stages but not in others. Use the ► toggle to open one of the three sections. Only the open section is active.
Field Description
Anatomical Structure The anatomical structures are taken from the Mouse Developmental Anatomy Browser. Begin typing a term of interest and an autocomplete list activates on the second character.

For each stage, the Anatomical Dictionary is organized as a hierarchy of structures. For the first field, Find genes where expression is detected in, the search includes substructures. This means that if you search for gene expression in, for example, brain, besides searching for brain, the system also searches for substructures to brain in the hierarchy, such as rhombencephalon.

You must enter a structure in both fields.

Please note:

If you are unsure of the most appropriate structural term to use, browse the Mouse Developmental Anatomy Browser.

Developmental Stage Use this field to select one or more Theiler stages (TS) to focus your search on a particular stage of embryonic development.
  • The default for the lower box is Any stages not selected above.
  • If you enter more than one stage in the upper box, for the query to return a particular gene, results demonstrating its expression must exist for at least one of the specified stages.
  • If you enter more than one stage in the lower box, the query returns those genes for which there was an absence of expression in Any stages not selected above.

Note: The Theiler system organizes development into stages defined by the appearance of specific developmental features. Embryos of the same gestational age can vary considerably with respect to development. Consequently, a Theiler stage does not precisely correspond to a particular age. For example, TS 21 applies to embryos between 12.5 and 14.0 days post conception (dpc), while TS 22 applies to embryos between 13.5 and 15.0 dpc. Therefore, if you are interested in all available records for embryos of age 14.0 dpc, you must select both TS 21 and TS 22.

You can browse Stage descriptions for a list of the defining features for each Theiler stage.

Structure and StageUse this section when you want to query for genes expressed in some structures and stages but not in other structures and stages. This section combines the query fields for the Anatomical Structure and Developmental Stage fields.

You must enter a structure in both fields.

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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. 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. If you modify your search, the filters are automatically applied to your modified results.

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How do I interpret the query results summary and detail pages?

See Interpreting Gene Expression Data Query Results.

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How do I distinguish genes whose expression was not detected from those that have not been analyzed?

A differential expression search returns a list of genes whose expression was shown to be absent (not detected), as well as genes whose expression has not been analyzed or recorded in the database for the specified structures and stages. If you filter for Detected?: No, the gene list will be limited to those genes whose expression was shown to be absent. Note: the filters apply to all data tabs.

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

Yes. The Genes and Assay Results tabs but not the Assays tab, 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?

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. If you click the Batch Query icon, the default Batch Summary will appear for your list of genes. Use the Click to modify search button to expand your search results to include additional information such as Gene Ontology (GO) terms, Mammalian Phenotype (MP) terms or Human Diseases associated with the genes.

See also Using the MGI Batch Query.

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Are there examples of query results?

The following examples give the field values required for each query when using the Differential Expression Search.

  1. What genes are expressed in the forebrain and not expressed in the midbrain?

    Anatomical Structure(s):   (upper box)   CONTAINS forebrain
    Anatomical Structure(s):   (lower box)    CONTAINS midbrain

    This query returns a summary page listing assay results for genes that have been shown to be expressed (detected=yes) in the forebrain (and its substructures) and whose assay results for the midbrain (and its substructures) were either lacking expression (detected=no) or have not been analyzed. By default, the summary opens with the list of genes. You can use the Assay results tab to distinguish between those genes for which expression has been demonstrated to be lacking and those that have not been analyzed.

  2. Which genes are expressed only at Theiler Stage 15?

    Developmental Stage(s):   (upper box)   TS 15
    Developmental Stage(s):   (lower box)    Any stages not selected above

    This query returns genes shown to be expressed exclusively at TS 15. For those genes, expression results obtained at any other Theiler stage must be Not detected (absent) or not analyzed.

  3. Which genes are expressed at Theiler Stage 10 but either are not expressed or have not been analyzed in the postnatal animal?

    Developmental Stage(s):   (upper box)   TS 10
    Developmental Stage(s):   (lower box)    TS 28

    This query returns genes that have been shown to be expressed in the TS 10 embryo but for which there are no positive (detected=yes) expression results at TS 28. For those genes, this is either because the results present in the database for the postnatal animal were either Not detected (absent) or did not exist (not analyzed).

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