FlyBase:Aberration Report

Last Updated: 8th July 2015

The Aberration Report provides information on individual chromosomal aberrations. Aberrations are chromosomal rearrangements that differ from the wild-type arrangement of chromosomes.

This is a field-by-field guide to the information that is provided in the Aberration Report.

FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data. The exception in the Aberration Report is the General Information section which contains a summary of the identity of the aberration and a summary of cytological data.

General Information

Symbol	The valid symbol that is used in FlyBase for the aberration. 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 aberration symbol is used throughout FlyBase. For D.melanogaster aberrations, the species prefix is only displayed in the General Information section at the top of a Report. See the General principles for naming aberrations section of the FlyBase Nomenclature document for a detailed description of how aberration symbols are constructed.
Name	The valid full name that is used in FlyBase for the aberration.
Feature type	A list of controlled vocabulary terms from the Sequence Ontology that describe the nature of the chromosomal aberration relative to the wild-type chromosomal order.
Also Known As	A list of up to 10 commonly used symbol synonyms for the aberration. (This list is made computationally, based on the frequency of alternative symbols that have been curated from the literature.). This field is only displayed on an individual Aberration Report if it contains data.
Species	The organism that the aberration originates from, with the initial letter of the genus and the full species name listed.
FlyBase ID	The Primary FlyBase identifier number of the aberration, used to uniquely identify the aberration in the database. An aberration may also have any number of Secondary FlyBase identifier numbers, which are listed in the Secondary FlyBase IDs section of the Aberration Report.
Computed Breakpoints include	Computed cytological breakpoints for the aberration, based upon data from the literature. See Computed cytological data in FlyBase for a detailed description of how these computed cytological breakpoints are calculated.
Deleted segment	The maximal cytological range of a segment that is deleted in the aberration. The statement reflects either observed cytology or cytology estimated from sequence coordinates.
Duplicated segment	The maximal cytological range of a segment that is duplicated in the aberration. The statement reflects either observed cytology or cytology estimated from sequence coordinates.
Genomic Maps
Sequence coordinates	The coordinates of aberration breakpoints. Sequence coordinates are reported by authors or inferred by FlyBase.
Member of large scale dataset(s)	If the aberration is a member of large scale dataset, the name of the dataset is listed here (hyperlinked to the relevant Large Dataset Metadata Report). A description of the attributes of the dataset is also present.

Nature of the Aberration

Cytological Order	A description of the new cytological order of the chromosomal aberration. The sequence of each chromosome involved in the chromosomal aberration is specified from one end to the other according to salivary gland chromosome band terminology. Each chromosome is separated by a semicolon. Points of breakage and reunion are indicated by vertical bars, and segments between these points are designated by the most extreme band known to be present at each end, separated by a dash. If the order of a particular segment is not known, the segment is included within parentheses, and hierarchies of ambiguities are represented by parentheses within parentheses. See the New order section of the FlyBase Nomenclature document for an example.
Progenitor	The mutant chromosome(s) on which the aberration was induced, where the progenitor is relevant to the derivative aberration. The progenitor is usually an aberration, a mutant allele or a transposable element insertion. Clicking on the symbol of the progenitor will take you to the relevant Report page.
Mutagen	A list of controlled vocabulary terms from the FlyBase controlled vocabulary that describe the origin of the chromosomal aberration, typically the mutagen(s) used to induce the chromosomal aberration.
Class of aberration (relative to wild type)	A list of controlled vocabulary terms from the Sequence Ontology that describe the nature of the chromosomal aberration relative to the progenitor chromosome.
Class of aberration (relative to progenitor)	A list of controlled vocabulary terms from the Sequence Ontology that describe the nature of the chromosomal aberration relative to the progenitor chromosome.
Breakpoints	A list of reported breakpoints for the aberration. See the Cytogenetic descriptions section of the FlyBase Nomenclature document for an explanation of the notation used by FlyBase for cytological breakpoints.
Causes alleles	A list of alleles caused by the aberration, due to a breakpoint within the locus. Clicking on an allele symbol will take you to the relevant Allele Report.
Carries alleles	A list of alleles that are carried on the aberration but are separable from its breakpoints. Clicking on an allele symbol will take you to the relevant Allele Report.
Transposon Insertions	A list of insertions of transgenic constructs or natural transposons that are carried on the aberration. The insertions listed can be either separable or inseparable from any of the breakpoints of the aberration. Clicking on an insertion symbol will take you to the relevant Insertion Report.
Formalized genetic data	A formalised summary listing breakpoints of the aberration ("bk1", "bk2" etc.) and their position relative to certain genes carried on the chromosome (these are not necessarily the genes that immediately flank the breakpoints). Each gene or breakpoint is listed in the order they are positioned along the chromsome, separated by the symbol "<<", which should be read as "lies to the left of". If a breakpoint is known to hit a certain gene, this is listed as for example "bk1 hits Sep1".
Genetic mapping information	Free text comments relating to genetic mapping information for the aberration.
Comments	Free text comments about the molecular nature of the aberration.
Comments on Cytology	Free text comments about the cytology of the aberration.
Sequence Crossreferences	A table of DDBJ/EMBL/GenBank sequence accession numbers relevant to the aberration. Clicking on the accession number will take you to the appropriate entry in the GenBank database.

Gene Deletion and Duplication Data

Genes Deleted/Disrupted

Complementation Data

Completely deleted / disrupted	A list of genes that have been reported to be completely deleted/disrupted by the aberration, as determined by genetic complementation analysis. This generally means that the aberration behaves as a null mutation for each gene in the list. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Partially deleted / disrupted	A list of genes that have been reported to be partially deleted/disrupted by the aberration, as determined by genetic complementation analysis. This usually means that the aberration behaves as a hypomorphic mutation for each gene in the list. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Molecular Data

Completely deleted	A list of genes that have been reported to be completely deleted by the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Partially deleted	A list of genes that have been reported to be partially deleted by the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Genes NOT Deleted/Disrupted

Complementation Data	A list of genes that have been reported not to be removed or broken by the aberration, as determined by genetic complementation analysis. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Molecular Data	A list of genes that have been reported not to be removed or broken by the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Genes Duplicated

Complementation Data

Completely duplicated

A list of genes that have been reported to be fully duplicated within the aberration, as determined by genetic complementation analysis. This usually means that the the duplication behaves as a wild type allele for each gene in the list. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Partially duplicated

A list of genes that have been reported to be partially duplicated within the aberration, as determined by genetic complementation analysis. This usually means that the the duplication provides some function for each gene in the list, but behaves as a hypomorphic mutation in each case. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Molecular Data

Completely duplicated	A list of genes that have been reported to be fully duplicated within the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Partially duplicated	A list of genes that have been reported to be partially duplicated within the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.

Genes NOT Duplicated

Complementation Data	A list of genes that have been reported not to be duplicated within the aberration, as determined by genetic complementation analysis. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Molecular Data	A list of genes that have been reported not to be duplicated within the aberration, as determined by molecular mapping. Clicking on a gene symbol will take you to the relevant Gene Report. This field is only displayed in an individual Aberration Report if it contains data.
Related Comments	Free text comments relating to both complementation analysis and molecular mapping information concerning the aberration.

Phenotypic Data

In combination with other aberrations	Free text description of the reported mutant phenotype of the aberration when in combination with other aberrations.
NOT in combination with other aberrations	Free text description of the reported mutant phenotype of the aberration (while not in combination with other aberrations), when the mutant phenotype cannot be attributed to individual genes that are broken or deleted by the aberration.

Stocks

Clicking on the "Search for Stocks" button allows you to search for stocks that contain the aberration.

Notes on Origin

Discoverer

A list of the individuals who identified or generated the aberration.

Free text comments about the origin of the aberration.

For example, information that it was simultaneously induced with another mutation/aberration, or information about the genotype of the progenitor which is irrelevant to the derivative.

Balancer/ Genotype Variants of the Aberration

A list of balancer and/or genotype variants of the aberration. Genotype variants carry the same chromosomal rearrangement as the aberration, but differ genetically, e.g. carrying a different constellation of alleles and/or transposable element insertions. A genotype variant chromosome may also be a Balancer, which is a multiply inverted chromosome that suppresses recombination with the homologous chromosome, allowing the homologous chromosome (or part of it) to be maintained intact in a cross or stock.

Clicking on the balancer/genotype variant symbol will take you to the relevant Balancer/Genotype variant Report.

Separable Components

A list of separable components of the aberration. These are chromosomal rearrangements that are derived from the parent aberration by non-mutagenic means. These component aberrations have properties that differ from those of the intact parent aberration.

For example, many transpositions can be separated into a deleted-chromosome component and a duplicated-chromosome component.

Clicking on the separable component symbol will take you to the relevant Aberration Report.

Other Comments

Miscellaneous free text comments about the aberration.

Synonyms and Secondary IDs

Reported As

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

Secondary FlyBase IDs

A list of Secondary FlyBase identifier numbers of the aberration.

If an aberration 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 the aberration, subdivided into fields by type of publication. Only those fields containing data are displayed in an individual Aberration Report.