Expression Pattern Annotations
Expression patterns for reporter constructs assayed in Drosophila melanogaster have been annotated using terms from the Drosophila gross anatomy ontology. Both the annotation and the ontology itself are works in progress, so care should be taken when making use of these data. Because expression patterns as described in the literature are not reported using the ontology terms, and are given in varying levels of detail, providing an exact description in the database is not always straightforward. We have provided these descriptions as a way to facilitate searching and grouping the included CRMs. However, we strongly encourage users to consult the notes included with our annotations as well as the original references for more detailed descriptions of expression patterns. In particular, note that the anatomy ontology does not always provide a means to distinguish sub tissue- or organ-level cell populations. Thus, two entries annotated as "wing disc" may in fact refer to non-overlapping cell types within the disc, two entries annotated as "ventral nerve cord" may refer to separate neuronal lineages, etc. Expression patterns are reported based on the textual descriptions given by the authors; we did not attempt to refine these descriptions based on our own analysis of published photographs. See also searching expression patterns.
As of REDfly v6.0, additional attributes are annotated along with expression patterns see Figure 3. Every listed expression pattern is linked with the stage(s) of development at which this expression is observed, and an indicator of whether that expression pattern is consistent with or ectopic to that of the assigned target gene. Sex-specific expression is indicated as either male-specific, female-specific, or "both". Terms from the Gene Ontology are included where appropriate to indicate regulatory elements that respond to specific signals or environmental cues (e.g., wound healing, hypoxia). Also, for each annotated expression pattern it is noted whether the CRM is acting as an "enhancer" (defined loosely as mediating positive expression) or as a "silencer."
For reporter constructs assayed in Drosophila melanogaster, developmental staging is provided using terms drawn from the Drosophila development ontology. Users should take note that stages are based on descriptions provided by the authors and are not necessarily comprehensive descriptions. Moreover, observed "off" stages may represent perdurance of a reporter gene rather than accurately reflect the continued activity of a CRM. In many cases, the "off" stage will be listed as "none." This indicates that no off stage has been described and is not meant to suggest that the CRM is indefinitely active. For purposes of searching the database, when no "off" stage is provided the off stage will be considered to be the end of the next major life-cycle stage following the "on" stage, i.e., end of embryogenesis, end of larval development, end of pupation, end of adulthood.
Note that this expanded attribute information is not yet available for all records. New records will contain the full set of attribute annotations, while older records will be updated over time.
Information for features assayed in species other than Drosophila melanogaster may be less complete, depending on the availability of anatomy and staging ontologies for that species.
Search and download functionality for these attributes will be phased in over time but is not yet available. However, the basic information can be viewed in the Expression tab of the Detailed view window for each record.
In general, TFBS records are not annotated with expression pattern information. However, if a TFBS is contained within an annotated RC/CRM, the TFBS will inherit expression pattern information from the related RC/CRM record. Note that in most cases, it has not been demonstrated that this particular TFBS plays a functional role in mediating any or all of the tissue-specific expression ascribed to the CRM.