This help document answers the following questions:
The Gene Expression Literature Query Form allows you to query for references that include data on endogenous gene expression in the mouse. The Gene Expression Database (GXD) curators create content records that contain information on the genes and ages analyzed and assay types used in each reference; the query form queries these content records. To the best of our knowledge, all publications containing embryonic expression data from 1993 to the present for all pertinent journals, and from 1990 to the present for the major development journals, have content records. However, expression assays using knock-in reporter genes have only been included in the content records since May 2002. Curators add content records to GXD weekly.
To search, enter or select values in one or more of the search 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.
|Gene Symbol/Name | Assay type | Age | Author | Journal | Year | Text|
|Gene Symbol/Name||Symbol, name, or synonym for a mouse genetic marker.
|Assay type||Selection list of assay types. Use this field to limit your search to assays of one or more selected types. The default operator is ANY.|
|Age||Days post conception of the specimen used in the reference. In addition to specific age values available on the drop-down list, there are also E and P.
|Year||The year the article was published. Use in conjunction with other fields to further narrow the scope of a search. Enter a year in the format 20XX. Enter a single year, a range of years, or an open-ended query such as everything after 2009 (2009-) or everything before 2007 (-2007).|
|Text||Enter a text string to search for articles with abstracts/titles containing the terms you enter.
Gene Expression Literature queries return a summary of search criteria matches. Each record appears in two areas: at the top of the page in the Summary by Age and Assay table and in the Summary by Gene and Reference listing.
A content record is created for each gene whose expression is analyzed in a reference. The details in a record are called the results. Each result reports the assay type used and the age of the specimen analyzed.
If you access a summary from ... a box at the top displays the ... Reference details Reference and its J number (linked to the full reference record) Marker details Symbol of the gene whose expression results are being summarized (linked to the marker detail record) and its name Gene Expression Data Query Results Parameters used to generate the query (supplied either from a query form or from a referring page) Links within the Summary by Age and Assay table Assay type and age of the chosen link
The Summary by Age and Assay table groups search criteria matches according to the age of the specimen analyzed and the assay type used for the analysis.
Links to subsequent details contain table listings of the symbol and name of the assayed gene (linked to the marker details), and the citation and J number of the expression results reference (linked to the full reference record). Then, if the reference has in depth annotations, the phrase Detailed expression data for these assays and the number of results appears, linked to the summary pages.
The lower portion represents expression information about the gene in the reference. A red ball indicates the assay types used and the ages analyzed; each ball represents a result. 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.
In addition to specific age values, two general annotations are used:
E Embryonic expression analyzed, exact age of tissue not specified in reference P Postnatal (includes adult) expression analyzed.
Any comments the curator feels are necessary to interpret the record appear at the bottom of the page. Note: As indicated on the detail page, the record denotes only that a gene was assayed for, using a particular assay type, and does not indicate whether or not gene expression was detected.