Search Pane

Basic search (see Figure 2A) allows for searching by gene name, FlyBase ID (FBgn), FlyBase FBtp number, element name, PubMed ID, or recent updates; the latter will return all records entered on the most recent date of data entry/update. Options to “browse all” records and to download all Reporter Constructs, all CRMs, or all TFBSs are also available.

By default, searches will not return Reporter Construct/CRM records discovered exclusively through cell-culture based assays (this is to prevent the results from being dominated by RCs proven to function in only a single cell type). To include these RCs/CRMs, uncheck the “Exclude Cell Line Only” box to the right of the “search” button.

Gene names should be searched as official FlyBase gene symbols (e.g., dpp, h, betaTub60D) or FlyBase IDs (e.g., FBgn0000490, FBgn0003888). Greek letters have been written out (e.g., alpha, delta). At present only valid primary gene symbols are accepted. If the name of a gene does not appear in the drop-down, it is likely that a synonym rather than the primary name is being used. In such cases, retrieving the proper name from FlyBase and searching again should resolve the problem. The gene name “unspecified” has been included to allow for searching for RCs or TFBSs where the associated gene or transcription factor, respectively, is not known.

If “by name” is selected, the search will retrieve only those records explicitly annotated with the gene name being searched. The default behavior is “by locus,” which will retrieve all records with the current gene name, but also all other Reporter Constructs/TFBSs within the defined region (default 10,000 bp upstream and downstream of the named gene). This allows for retrieval of Reporter Constructs annotated as “unspecified” and those lying near a gene of interest but annotated as being associated with a different gene. The size of the genomic region to be searched can be modified using the “search range interval” box under Advanced Search. (Similar behavior can be achieved by using coordinates to specify a genomic region to search using the location search features in the Advanced Search area.)

A wild-card is automatically appended to the end of the search string for all element name searches (e.g., searching for “eve_stripe” will return “eve_stripe1”, “eve_stripe2”, “eve_stripe3+7”, etc.).

Basic search (see Figure 2A) allows for searching by gene name, FlyBase ID (FBgn), FlyBase FBtp number, element name, PubMed ID, or recent updates; the latter will return all records entered on the most recent date of data entry/update. Options to “browse all” records and to download all Reporter Constructs, all CRMs, or all TFBSs are also available.

By default, searches will not return Reporter Construct/CRM records discovered exclusively through cell-culture based assays (this is to prevent the results from being dominated by RCs proven to function in only a single cell type). To include these RCs/CRMs, uncheck the “Exclude Cell Line Only” box to the right of the “search” button.

Gene names should be searched as official FlyBase gene symbols (e.g., dpp, h, betaTub60D) or FlyBase IDs (e.g., FBgn0000490, FBgn0003888). Greek letters have been written out (e.g., alpha, delta). At present only valid primary gene symbols are accepted. If the name of a gene does not appear in the drop-down, it is likely that a synonym rather than the primary name is being used. In such cases, retrieving the proper name from FlyBase and searching again should resolve the problem. The gene name “unspecified” has been included to allow for searching for RCs or TFBSs where the associated gene or transcription factor, respectively, is not known.

If “by name” is selected, the search will retrieve only those records explicitly annotated with the gene name being searched. The default behavior is “by locus,” which will retrieve all records with the current gene name, but also all other Reporter Constructs/TFBSs within the defined region (default 10,000 bp upstream and downstream of the named gene). This allows for retrieval of Reporter Constructs annotated as “unspecified” and those lying near a gene of interest but annotated as being associated with a different gene. The size of the genomic region to be searched can be modified using the “search range interval” box under Advanced Search. (Similar behavior can be achieved by using coordinates to specify a genomic region to search using the Location Search features in the Advanced Search area).

A wild-card is automatically appended to the end of the search string for all element name searches (e.g., searching for “eve_stripe” will return “eve_stripe1”, “eve_stripe2”, “eve_stripe3+7”, etc.).

The Advanced Search pane (see Figure 2B) is divided into two tabs, one for Reporter Construct/CRM options and one for TFBS options.

RC/CRM Options

These include searching for all records, for CRM records only, for CRMs with associated TFBS data only, or for “inferred CRMs”. These can be further filtered for positive vs. negative expression and for whether or not an element has undergone minimization.

TFBS Options

These allow for searching all TFBSs or only those with associated CRM data. Gene names can be used to search all TFBS records or only those where the named gene is either the target or encodes the transcription factor, respectively.

Details on search options are as follows:

Position

Position search is currently under development and will not return complete results.

Position search will select any RCs/CRMs or TFBSs located in the specified position relative to their target gene. Options are 5’ to the gene, 3’ to the gene, within an intron, or within an exon. Options are non-exclusive, i.e., a RC that begins 5’ to the gene and extends through the first intron will be found by a search for any of 5’, intron, or exon.

To be considered as overlapping a genomic feature, a regulatory element must extend greater than five bp into that feature. Thus, a CRM in the proximal promoter region that begins 500 bp 5’ to the transcription start of its gene and extends two bp into the first exon is considered to be exclusively 5’ to the gene and will not be returned on a search for elements within exons.

Positional information is reported in the detailed view window in the Location tab.

Location search will select any RCs/CRMs or TFBSs lying within the specified sequence range, using release 6/dm6 coordinates. Coordinates from older releases can be converted through FlyBase’s “Coordinates Converter” tool.

Search Range Interval

Search Range Interval sets the size of the genomic region to be searched when the Basic Search “by locus” option is selected. Default is 10,000 bp.

Maximum Size

Selecting a maximum size will exclude any RCs/CRMs or TFBSs whose length is greater than the specified value, in basepairs.

Restrict Evidence To

This field allows the user to restrict a search to sequences supported by only certain types of evidence, e.g., TFBSs supported by DNAse I footprinting only.

Last Updated After/Date Added

Placing a value in these fields will restrict the search results to those records that have been added or updated on or after the chosen date, respectively. Use the Last Updated feature to check for additions and corrections since your last search.

Searching Expression Patterns

Two methods of expression pattern searching have been implemented in REDfly. Searching using the Ontology/Expression Term search field will select records containing the specified term or any of the descendant terms in the ontology hierarchy; checking the “exact term” box will restrict the search to only that term. The Ontology search function therefore provides a way to identify RCs/CRMs that potentially drive similar spatial patterns of expression despite that expression having been described at different levels of detail in the literature. Ontology searching can be conducted either by entering an ontology term in the search box, or by selecting a term from the pop-up Ontology Browser. The search box incorporates a search widget from the National Center for Biomedical Ontology that converts synonyms to preferred terms. For example, typing “wing disc” will automatically bring up “dorsal mesothoracic disc” as the top option in the drop-down.

See also Expression Pattern Annotations.

For example, searching for "mesoderm" using the Expression Term search will return annotations such as

  • FBbt:00000126, mesoderm
  • FBbt:00000128, trunk mesoderm
  • FBbt:00000130, visceral mesoderm
  • Using "exact match," only

FBbt:00000126, mesoderm would be returned.

A search for "mesoderm" using the Ontology Search would return records with the same terms as above, but also with terms such as

  • FBbt:00000126, mesoderm
  • FBbt:00000128, trunk mesoderm
  • FBbt:00000130, visceral mesoderm
  • FBbt:00005073, somatic muscle
  • FBbt:00000466, oblique muscle
  • FBbt:00005247, hemocyte primordium
  • FBbt:00001666, cardioblast

and so forth. With “exact term” checked, only records explicitly annotated as FBbt:00000126, mesoderm will be returned.

In practice, Exact Term searches will often be too restrictive, and the full Ontology search too permissive. In the future, we hope to improve the Ontology search function to allow greater control over the depth of the search. Users may find it helpful to examine the FlyBase Gene Expression section for aid in navigating the Ontology.

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