New Release: FB2015_01, released February 24th, 2015
FB2015_01, released February 24th, 2015
 
 

A Database of Drosophila Genes & Genomes

Gene Expression report help

Last Updated: 22 November 2006

This is a field-by-field guide to the information provided on the Gene Expression Report

FlyBase strives to link curated information about a gene's expression to particular protein and transcript species. However, in most cases, it is not possible to attribute a characteristic to an individual gene product. For example, expression pattern data is often obtained with probes or antibodies that recognize more than one product of a gene. It is not rigorously known where each individual gene product is expressed. In addition, it is often not possible to determine which transcript observed on a northern blot corresponds to a particular cDNA. Therefore, the Gene Expression Report is a central location where all curated information about a gene's expression can be stored without necessarily attaching such information to a particular product of that gene. Where such information is available, however, it is indicated.

Note:

In versions of FlyBase prior to the FB2006_01 release (see the Archives section of the Navigation bar), expression pattern information that could not be attributed to a particular transcript or polypeptide was stored in a "generic transcript" or "generic polypeptide" report. These generic transcripts and polypeptides were given the suffix -XR and -XP. Generic transcripts and polypeptides are no longer used by FlyBase, and instead the Gene Expression Report serves as the location for all expression information.

hide General Information
Symbol

The valid symbol that is used in FlyBase for the gene.

The first part of the symbol (before the '\') is the standard prefix for the species (from the Species Abbreviations list). For species other than D.melanogaster, the species prefix is displayed wherever the gene symbol is used throughout FlyBase. For D.melanogaster genes, the species prefix is only displayed in the GENERAL INFORMATION section at the top of a Report.

Name

The valid full name that is used in FlyBase for the gene.

Feature type

A single controlled vocabulary term from the Sequence Ontology (SO), which aims to describe the key type of the gene.

The single term in this field is computed by FlyBase from the full list of SO terms listed in the SEQUENCE ONTOLOGY: Class of gene section of the Gene Report.

See Computed Feature type of genes for a detailed description of how the term is selected.

Created/Updated

The date that the gene was entered into the chado database underlying FlyBase (we migrated to the chado database on 2006-08-22) and the date that the gene report was last updated. The dates are in the format: year-mm-dd.

Species

The organism that the gene originates from, with the initial letter of the genus and the full species name listed.

Annotation symbol

The current symbol for the annotation that represents the gene.

!!perhaps there should be doc defining what an annotation is, and the word "annotation" above could link to that!!

!!do we need, "if it exists" equivalent, as not every gene has an annotation!!.

FlyBase ID

The Primary FlyBase identifier number of the gene, used to uniquely identify the gene in the database.

A gene may also have any number of Secondary FlyBase identifier numbers, which are listed in the SECONDARY FLYBASE IDs section of the Gene Report.

hide Transcript Expression
Expression Data

A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by locaton of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages are described using controlled vocabulary (CV) terms.

Additional Descriptive Data

Free-text curated descriptions of expression patterns, sorted by reference.

Assay Mode

Method used to obtain the expression pattern data used in a particular reference. Common assay modes are in situ hybridization and Northern blot.

Marker for

The expression of some genes is used as a marker for a particular tissue or developmental state. If that data exists for a gene, the name of the body part would be listed here.

Subcellular Localization

Some transcripts are described as being localized to a particular part of a cell, for example, the mitochondrion. If such data exists for transcripts of a gene, it is listed in this field.

CV Term

A list of Gene Ontology (GO) cellular component terms that describe the subcellular location of the transcript or transcripts of this gene.

Notes

The information in this field is free-text curated descriptions of subcellular expression patterns, sorted by reference. In previous version of FlyBase (see Release 4.3), this information was stored in a field called "Cell location summary" on the generic transcript (-XR) reports.

hide Polypeptide Expression
Expression Data

A three column table with the headings Stage, Tissue/Position, and Reference. Each row in the table represents one distinct expression pattern defined by time of expression (Stage) and by locaton of expression (Tissue/Position). Each distinct expression pattern is attributed to the reference that reported it. Developmental stages are described using controlled vocabulary (CV) terms.

Additional Descriptive Data

The information in this field is free-text curated descriptions of expression patterns, sorted by reference. In the previous version of FlyBase (see Release 4.3), this information was stored in a field called "Expression Info" on the generic polypeptide (-XP) reports.

Assay mode

Method used to obtain the expression pattern data used in a particular reference. Most commonly for a polypeptide the assay mode will be immunolocalization.

Marker for

The expression of some genes is used as a marker for a particular tissue or developmental state. If that data exists for a gene, the name of the body part would be listed here.

Subcellular Localization

Some polypeptides are described as being localized to a particular part of a cell, for example, the mitochondrion or the plasma membrane. If such data exists for polypeptides of a gene, it is listed in this field.

CV Term

A list of Gene Ontology (GO) cellular component terms that describe the subcellular location of the polypeptide or polypeptides of this gene.

Notes

Free-text curated descriptions of subcellular expression patterns, sorted by reference. In previous version of FlyBase (see Release 4.3), this information was stored in a field called "Cell location summary" on the generic transcript (-XR) reports.

hide References

A list of publications that discuss the gene's expression pattern, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Gene Expression Report. For all references discussing the gene, see the References section of the Gene Report.