Difference between revisions of "FlyBase:Experimental Tool"

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Experimental Tool Report
 
Experimental Tool Report
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Experimental Tool reports are made for commonly used sequences with useful properties that are exploited to study the biological function of another gene product or a biological process. These include tools that enable a gene product to be detected (e.g. the FLAG tag, EGFP, mCherry), target a gene product somewhere specific within a cell (e.g. nuclear localisation signal, signal sequence), drive expression in a binary system (e.g. UAS, GAL4) or enable clonal/conditional expression (e.g. FLP, FRT). Each Experimental Tool report provides a description of the tool and its uses, together with browsable tables of transgenic constructs that encode or carry that tool.
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==General Information==
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{| class="wikitable" style="width: 100%;"
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|-
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| '''Symbol''' || The FlyBase symbol for the experimental tool.
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|-
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| '''Name''' || The FlyBase full name for the experimental tool.
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|-
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|-
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|-
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| '''FlyBase ID''' || The unique identifier for the FlyBase experimental tool (FBto number).
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|}
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==Description==
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{| class="wikitable" style="width: 100%;"
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|-
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| '''Description''' || style="width: 80%;" | A short textual description of the experimental tool, written by FlyBase curators based on the given reference(s).  References are hyperlinked to their respective Reference Report in FlyBase or to PubMed.
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|-
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| '''Uses''' || One or more [[FlyBase:Controlled_vocabularies_used_by_FlyBase|controlled vocabulary]] terms that describe how the experimental tool is used.
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|-
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| '''Notes''' || Free text comments that generally highlight unusual/unexpected observations about a tool that do not fit into the general description field.
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|-
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| '''External Crossreferences and Linkouts''' || Links to information for this experimental tool available from external web sites.
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|}
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==Related experimental tools==
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{| class="wikitable" style="width: 100%;"
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|-
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| '''Common gene of origin''' || style="width: 80%;" | A list of tools (and their uses) that have the same gene of origin as the tool that is the subject of the report. For example, in the EGFP report, this field lists other fluorescent variants derived from GFP that have been used as tools in transgenic flies.
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| '''Compatible tools''' || If the tool forms part of a multi-component experimental system (e.g. binary or split expression systems) or is part an enzyme/target site pair, this field will list those tools that are compatible with the tool that is the subject of the report. Both the symbol and uses of the compatible tools are listed. For example, the GAL4 tool lists UAS and GAL80 in this field (and vice versa).
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| '''Other''' || A list of other related tools and their uses, that do not fit into either the 'Common gene of origin' or 'Compatible tools' categories.
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|}
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==Transgenic Constructs==
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A table listing Transgenic constructs that encode or carry the tool. The different components of the construct are listed in separate columns, in addition to a column listing the number of stocks.
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The tables are subdivided as follows, according to which component of the construct the tool corresponds to.
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{| class="wikitable" style="width: 100%;"
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|-
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| '''Encodes tool''' || style="width: 80%;" | The experimental tool is the 'main' gene product encoded by the construct.
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|-
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| '''Tagged with the tool''' || The experimental tool 'tags' another gene product whose biological function is being studied.
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| '''Carrying the tool''' || The experimental tool is carried within the construct, but does not form part of the encoded gene product.
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| '''Has tool as regulatory region''' || The experimental tool is carried within the construct, and acts as a regulatory region that drives transcription either of the gene product encoded by the construct, or in the case of misexpression elements such as P{EP}, of neighboring genomic loci when the element is inserted in the genome.
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|}
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Where applicable, columns have a 'Show/Hide Uses' toggle at the top which can be used to show/hide the 'Uses' controlled vocabulary terms that describe how each experimental tool in the column is used.
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==Synonyms & Secondary IDs==
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===Reported As===
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{| class="wikitable" style="width: 100%;"
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|-
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|'''Symbol Synonym''' || style="width: 80%;" | A list of symbols that have been commonly used in the literature, or used by FlyBase, to describe the experimental tool.
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|'''Name Synonym''' || A list of names that have been commonly used in the literature, or used by FlyBase, to describe the experimental tool.
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|}
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===Secondary FlyBase IDs===
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A list of Secondary FlyBase identifier numbers of the tool.
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If an experimental tool has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.
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==References==
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A list of publications that discuss or use the experimental tool, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual experimental tool report.

Latest revision as of 10:53, 24 August 2018

Experimental Tool Report

Experimental Tool reports are made for commonly used sequences with useful properties that are exploited to study the biological function of another gene product or a biological process. These include tools that enable a gene product to be detected (e.g. the FLAG tag, EGFP, mCherry), target a gene product somewhere specific within a cell (e.g. nuclear localisation signal, signal sequence), drive expression in a binary system (e.g. UAS, GAL4) or enable clonal/conditional expression (e.g. FLP, FRT). Each Experimental Tool report provides a description of the tool and its uses, together with browsable tables of transgenic constructs that encode or carry that tool.

General Information

Symbol The FlyBase symbol for the experimental tool.
Name The FlyBase full name for the experimental tool.
FlyBase ID The unique identifier for the FlyBase experimental tool (FBto number).

Description

Description A short textual description of the experimental tool, written by FlyBase curators based on the given reference(s). References are hyperlinked to their respective Reference Report in FlyBase or to PubMed.
Uses One or more controlled vocabulary terms that describe how the experimental tool is used.
Notes Free text comments that generally highlight unusual/unexpected observations about a tool that do not fit into the general description field.
External Crossreferences and Linkouts Links to information for this experimental tool available from external web sites.

Related experimental tools

Common gene of origin A list of tools (and their uses) that have the same gene of origin as the tool that is the subject of the report. For example, in the EGFP report, this field lists other fluorescent variants derived from GFP that have been used as tools in transgenic flies.
Compatible tools If the tool forms part of a multi-component experimental system (e.g. binary or split expression systems) or is part an enzyme/target site pair, this field will list those tools that are compatible with the tool that is the subject of the report. Both the symbol and uses of the compatible tools are listed. For example, the GAL4 tool lists UAS and GAL80 in this field (and vice versa).
Other A list of other related tools and their uses, that do not fit into either the 'Common gene of origin' or 'Compatible tools' categories.


Transgenic Constructs

A table listing Transgenic constructs that encode or carry the tool. The different components of the construct are listed in separate columns, in addition to a column listing the number of stocks.

The tables are subdivided as follows, according to which component of the construct the tool corresponds to.

Encodes tool The experimental tool is the 'main' gene product encoded by the construct.
Tagged with the tool The experimental tool 'tags' another gene product whose biological function is being studied.
Carrying the tool The experimental tool is carried within the construct, but does not form part of the encoded gene product.
Has tool as regulatory region The experimental tool is carried within the construct, and acts as a regulatory region that drives transcription either of the gene product encoded by the construct, or in the case of misexpression elements such as P{EP}, of neighboring genomic loci when the element is inserted in the genome.

Where applicable, columns have a 'Show/Hide Uses' toggle at the top which can be used to show/hide the 'Uses' controlled vocabulary terms that describe how each experimental tool in the column is used.


Synonyms & Secondary IDs

Reported As

Symbol Synonym A list of symbols that have been commonly used in the literature, or used by FlyBase, to describe the experimental tool.
Name Synonym A list of names that have been commonly used in the literature, or used by FlyBase, to describe the experimental tool.

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the tool.

If an experimental tool has a secondary identifier number, it generally indicates that at some point it has been merged with or split from other entries in the database. See the FlyBase identifier numbers section for some examples of the cases where identifier numbers are made secondary.

References

A list of publications that discuss or use the experimental tool, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual experimental tool report.

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