Using the Gene Expression Data Query Form

This help document answers the following questions:

• What is the purpose of the Gene Expression Database?
• What can I use the Gene Expression Data Query Form to find?
• How do I use this form?
• What values are acceptable in each of the query form fields?
• Can I edit my original options and requery?
• How do I interpret the query results summary and detail pages?
• What if the search does not find any expression results?
• Why is there a link to Gene Expression Literature records in my query summary?
• Which expression data query parameters generate an expression literature search? Which do not?
• Can I get my results as tab-delimited text or spreadsheet files?
• Can I send the results of my search to the MGI Batch Query?
• Are there examples of query results?

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 GXD.

See also the MGI Glossary for unfamiliar terms and acronyms.

What can I use the Gene Expression Data query form to find?

The Gene Expression Data Query form Standard Search tab allows you to ask questions that can be basic or complex. Examples of the type of questions you can ask are:

• When and where is En1 expressed?
• What genes are expressed in the heart at E8.5?
• Is Htr7 expressed in the brain?
• What genes are known not to be expressed in either the diencephalon or any structure containing the diencephalon?
• What genes involved in cell adhesion are expressed in mesenchyme?

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

If you are interested in doing queries that ask what genes are expressed in some anatomical structures and/or developmental stages but not in others, you should use the Gene Expression Data Expanded Query Form.

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 table. After entering values in the query form fields, click Search to submit the query. Click Reset to clear the fields and return any default values. See Using MGI Query Forms for answers to questions such as:

• How do I submit a query?
• Does it matter what case I use when I type values in the fields?
• Is there a way to speed up a query?

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What values are acceptable in each of the query form fields?

Genes | Anatomical structure or stage | Mutant / wild type | Assay types

Genes	This section offers a choice of two fields. Nomenclature search. Use the left hand field to search for expression data for a mouse gene or set of genes with a similar nomenclature. The gene nomenclature field supports an asterisk as a wild card. A search for pax* finds expression data for gene symbols and names that begin with pax. A search for *box* looks for nomenclature that contains box. This search finds the arginine decarboxylase gene, homeobox genes and paired box genes. A search for growth factor finds nomenclature containing growth AND factor. Synonyms (unofficial gene names used in publications and former official gene symbols) are also searched. This field searches only alphanumeric characters. Single and double quotes, commas and hyphens are ignored. Vocabulary term search. Use the right hand field to find expression data for genes defined by their function, phenotype or disease model association. Begin typing a term of interest and an autocomplete list activates on the second character. The list shows all the vocabulary terms and their synonyms that match your search characters (shown in bold letters) and the number of genes annotated to each term. Terms are greyed out if there are no genes annotated to the term or if there are no expression data associated with the genes. You can type the beginnings of multiple terms to narrow the list (example: axon guid). You must select a term. There is no free text searching in this field. You can only select one term, though choosing a term includes results for its subterms. For example, selecting decreased bone mass also includes results for its subterms, decreased compact bone mass, decreased trabecular bone mass and osteoporosis. The autocomplete field ignores non-alphanumeric characters such as " and -. If you are unsure of the proper terms to use, use the appropriate browser to find vocabulary terms and their definitions: Function: GO Browser Phenotype: Mammalian Phenotype Browser Disease: Human Disease Vocabulary Browser Note that you may not submit a search with values in the Nomenclature search and the Vocabulary Term search at the same time.
Anatomical structure or stage	Click to limit your search to assay results where expression was detected in, not detected in, or either. The default value is either. Detected in and not detected in both return results labeled Ambiguous and Not specified. You can choose to use one or both fields in this section. Anatomical Structures The anatomical structures are taken from the Anatomical Dictionary. Begin typing an anatomy term of interest and an autocomplete list activates on the second character. The list shows all the anatomy terms and their synonyms that match your search characters. You must choose a term from the autocomplete list (i.e., there is no free text entry in this field). For each developmental stage, the Anatomical Dictionary is organized as a hierarchy of structures. By default, the search includes substructures. This means if you search for gene expression in, for example, brain, this searches for all terms that contain the word brain and the substructures to those terms in the hierarchy, such as rhombencephalon. If you are unsure of the most appropriate structural term to use, browse the Anatomical Dictionary. Developmental Stages (dpc) Use this field to select one or more Theiler stages (TS) to focus your search on a particular stage of embryonic development. Alternately, you can choose the Use Ages tab and limit your search to the general terms, Embryonic or Postnatal, or choose days post conception (dpc). 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. To select multiple stages or ages: On a Macintosh, hold the command (Apple, ⌘) key down and click on the desired stages; OR hold the shift key down and click on two stages to select those and all stages in between. On a PC, hold the control key down and click on the desired stages; OR hold the shift key down and click on two stages to select those and all stages in between. If you mouse-over a stage, a pop-up will describe a few defining features of that stage, such as "first somites, late head fold" for Stage 12. You can browse Stage descriptions for a list of the defining features for each Theiler stage. Please note that in GXD all annotations of postnatal animals use Theiler Stage 28.
Mutant / wild type	Select Specimens mutated in gene to search for expression data obtained from mutant specimens. Use this field to enter the symbol or name of the mutated genetic marker. The system searches for current symbols/names and synonyms of the mutated gene. Use this search field as you would the Genes' nomenclature search at the top of the search form. Select Wild type specimens only if you wish to exclude mutant alleles from your search. This search will still include knock-in reporter genes used in in situ reporter assays. Select All specimens, the default, to include all mutant and wild type specimens in your search.
Assay types	Check list of assay types. Use this section to limit your search to assays of one or more selected types. The default is to search All of the assay types on the list. Uncheck the first box for Find expression data in any assay type to quickly clear all selections.

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Can I edit my original options and requery?

Yes, you can.

• If you want to edit a list or change output options:
1. When your results appear, click the banner at the top of the page (Click to modify search). (The banner title changes to Click to hide search.) The window that appears contains your original search criteria.
2. Make your changes.
3. Click Search.
4. Repeat until the desired results appear.

Notes:

• You can requery as many times as you like.
• Alternatively, click Reset to return to the original Gene Expression Data Query form.

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

Your search results are displayed within three tabs, each noting the number of results: Genes, Assays and Assay Results. By default, the Assay Results tab is selected.

Genes

If you select the Genes tab, the query summary contains the following fields:

MGI ID	MGI accession ID for the Gene
Gene	Symbol of the analyzed gene, linked to its MGI marker detail record
Gene Name	Name of the analyzed gene
Type	Marker feature type for the analyzed gene. See Genome Feature Type Definitions.
Chr	Chromosome to which the marker is assigned. Aside from a chromosome number, other possible values include MT (mitochondrial), XY (XY pseudoautosomal), UN (chromosome assignment is not known)
Genome Location-NCBI Build #	Genome coordinate range in base pairs and the build number of the B57BL/6J genome
Strand	Coding strand for the gene

By Assay

If you select the Assays tab, the query summary contains the following fields:

Gene	Symbol of the analyzed gene.
Assay Details	The word data links to detailed expression results; the MGI accession ID of the assay (useful for searching purposes) appears in parentheses. A camera icon appears when there are image data associated with the assay.
Assay Type	Name of the assay used (e.g., Immunohistochemistry, Northern blot, RNA in situ, and so on).
Reference	J number (MGI identifier) and short format citation for this reference linked to its MGI reference detail report.

Assay Results

If you select Assay Results, the query summary contains the following fields:

Gene	Symbol of the analyzed gene
Result Details	The word data links to detailed expression results; the MGI accession ID of the assay (useful for searching purposes) appears next in parentheses
Assay Type	Name of the assay used (e.g., immunohistochemistry, Northern blot, RNA in situ)
Anatomical System	High-level term for the anatomical system assayed (e.g. Cardiovascular System, Extraembryonic Component)
Age	Age of the specimen used in the assay. Whenever possible, the age annotations are normalized according to the following conventions: noon of the day on which the vaginal plug is found is counted as embryonic (E) day 0.5. Therefore, e.g., if an author refers to the day on which the plug is found as E0, we add 0.5 to the age value(s) listed in the paper and the comment Age normalized so that noon of plug day = E0.5 to the record. If the staging criteria are not described in the paper, we annotate to the ages given by the authors and may add the comment Age of embryo at noon of plug day not specified in reference to the record. The abbreviations for age annotations are as follows: E Embryonic day P Postnatal or postnatal day P week Postnatal week P month Postnatal month P year Postnatal year P adult Postnatal adult P newborn Postnatal newborn
Structure	Structure examined in the assay, given as a Theiler stage (TS) and anatomical structure name
Detected?	Was expression detected? Possible values include: Yes No Ambiguous Not specified Note: Not specified is used when the authors do not report whether a gel band is present or absent. Ambiguous is used when the curators cannot discern from the authors’ description whether expression is present or absent.
Figure(s)	The pane that illustrates the expression results. If we have permission from the publisher to use the images, this is linked to the figure(s)
Mutant Allele(s)	If the specimen is a mutant, the allele pairs describing the mutant genotype appear in this field.
Reference	J number (MGI identifier) and short format citation for this reference linked to its MGI reference detail report

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What if the search does not find any expression results?

See Interpreting Gene Expression Data Query Results.

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Why is there a link to Gene Expression Literature records in my query summary?

At the end of the query summary, there may be a link to Gene Expression Literature content records matching the parameters of your detailed expression data search.

• The first step of annotation in GXD is to create literature content records containing information on the genes and ages analyzed and assay types used in each reference. All expression papers have content records.
• The next step is for the curators to extract the detailed expression data from these references. The types of data annotated at this stage include: the anatomical structures analyzed; the authors' description of the pattern and strength of expression; and the genetic origin of the sample. Because annotation process is time-consuming, not all expression references have detailed data in the database.

Thus, to ensure that your query returns all the references of interest to you, searches of the detailed expression data also include searches of the literature content records (whenever query parameters apply to both these types of data).

Which expression data query parameters generate an expression literature search? Which do not?

The following detailed expression data query parameters generate an expression literature search:

• gene symbol/name
• function, phenotype or disease term
• developmental stage
• assay type.

Because of the limited annotation of content records, the following parameters do not generate an expression literature search:

• anatomical structure
• detected in (expression present)
• not detected in (expression absent)
• mutated gene symbol/name

Note: You can query gene expression literature content records directly using the Gene Expression Literature Query Form.

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Can I get my results as a spreadsheet file?

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 list the field values to set on the Gene Expression Data Query Form to perform each query. Leave the default values in all other fields.

1. When and where is En1 expressed?

   Genes…Search for expression data for…: en1
   

   This query returns a list of results from assays examining En1 expression. This summary report includes the gene symbol, result details linked to an assay record (click data), the assay type used, the age of the specimen, the structure examined, an indication of whether or not expression was detected, the mutant allele pairs describing the mutant genotype of the specimen (if applicable), and the reference from which the data were curated, linked to its abstract.

2. What genes are expressed in the heart at E8.5 in wild-type mice only?

   Expression: detected in
   Anatomical Structures: heart
   Developmental Stages (dpc): Select the Ages (dpc) tab and then E8.5
   Mutant / wild type:   Wild type specimens only
   

   This query returns a list of assay results for genes expressed in the heart at E8.5. Click the Genes tab to view a summary report that includes the gene symbols (with links to MGI detail pages), gene types and genomic map coordinates. The report does not include any expression results obtained from mutant alleles. Note: Each developmental stage in the example includes coverage of embryonic day 8.5. See Theiler System for details.

3. What members of the Wnt gene family are expressed in TS 16?

   Genes…Search for expression data for…:wnt*
   Expression: detected in
   Developmental Stages (dpc): TS 16
   

   This query returns a list of assay results for Wnt family genes whose expression was detected in Theiler Stage 16.

4. When and where are genes involved in axon guidance expressed?

   Genes…A set of genes defined by: axon guidance
   

   This query returns a list of all assay results for all genes known to be involved in mouse axon guidance.

5. What genes have NOT been shown to be expressed in either the diencephalon or any structure within the diencephalon?

   Expression: not detected in
   Anatomical Structure(s): diencephalon
   

   This query returns a list of genes found not to be expressed in the diencephalon or in anatomical structures within the diencephalon, such as the hypothalamus, 3rd ventricle, or pituitary gland.

6. What genes involved in cell adhesion are expressed in stomach mesenchyme?

   Genes...A set of genes defined by: cell adhesion
   Expression: detected in
   Anatomical Structures: stomach mesenchyme
   

   This query returns a list of genes involved in cell adhesion found to be expressed in the stomach mesenchyme.

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