Two types of data are accessible from the text searches:
1) expression data from whole mount in situ hybridization using alkaline
phosphatase (AP) staining and 2) confocal analysis using fluorescence in situ
hybridization and immunostaining. The Gene and Category searches return data
from AP in situ while the Confocal Data Search returns data from confocal
Gene Search - This
search is used to find information about a specific gene. Type the name, symbol,
or CG number for a gene and press the 'Search' button. If a gene is
retrieved, its information will show up in the results window below.
If you are unsure about the name of a gene, use the wild-card search to search all entries that
contain your text query. If multiple genes are returned, a list will appear
allowing you to choose the appropriate gene. From the results window you will be
able to select 'Details', 'Images', or 'Confocal'. Selecting 'Details' will take
you to the gene data page that contains much of the relevant data for
the gene, 'Images' brings you to the AP image display page,
'Confocal' brings you to the confocal data display page.
To search for multiple genes, use the batch
search. The text query box will enlarge to enter large numbers of gene
names, symbols, or CG numbers. A semicolon (;) should be used to separate
queries, but no other punctuation. Gene names, symbols, or CG numbers can be
mixed. For example: sim; VGlut; CG8394; abrupt; D; CG13565. Like the wild-card
search, if multiple records are returned, a list will appear and you can choose
the gene in which you are interested.
Category Search -
This search provides a list of genes derived from the AP expression data that
meet specific criteria. The criteria are defined using the context-sensitive
dropdown lists. First, choose the top-level criteria (Category). This will
automatically fill the second-level dropdown list (Subcategory). If additional
criteria are available, they will be listed in the third-level criteria dropdown
list. Once the criteria have been defined, pressing the 'Search' button
will show the search results. In some cases, expression was uncertain, these
genes can be included in the search by clicking the include potential expression checkbox.
Confocal Data Search -
The Confocal Data Search retrieves confocal expression
data from the database. The Confocal Search page is divided into 3 areas; 1) the
Query Building Tool (top left), 2) the query (top right), and
3) the results (bottom). The Query Building Tool has 5 tabs each representing
a different stage of midline cell development. Clicking on a tab will
reveal buttons corresponding to the midline cell types present at that stage.
Pressing a cell type button adds that cell type to the query. Parentheses should be used when formulating complex queries with
multiple terms (see below). Pressing the 'Back' button will remove the text
most recently added to the query and the 'Reset' button clears the query. Once
the query is assembled, pressing the 'Submit Query' button will return
the results in the results area.
Notes on generating complex queries:
Once a cell type is selected, you can then choose a
logical operator (AND, OR, NOT) to combine different cell types in a single
complex query. By default, the server processes logical operators in a specific order. First NOT, then AND, then OR
regardless of the order in which they appear in the query. To ensure you get the results you are looking for in complex queries,
parentheses should be used to specify the order in which the logical operators are applied.
For example, if you want to see all of the genes expressed at stage 13 in the H-cell and the H-cell sib,
that are not expressed in mVUM4, mVUM5, or mVUM6 the following query will not return the intended results:
'H-cell at stage 13 AND
H-cell sib at stage 13 BUT NOT mVUM4 at stage 13 OR mVUM5 at stage
13 OR mVUM6 at stage 13'
This query will return the intended results:
'(H-cell at stage 13 AND
H-cell sib at stage 13) BUT NOT (mVUM4 at stage 13 OR mVUM5 at stage
13 OR mVUM6 at stage 13)'