dictyBase Help: Gene Page
Contents
The Gene Page provides extensive information about a given gene, including
links to all its associated sequences, such as Curated Models, Gene Predictions, GenBank Sequences, and ESTs.
The Gene Page also links to additional dictyBase resources such as the Genome Browser, BLAST Server, and to external databases.
The dictyBase Gene Page is divided into several sub-sections. The different sections are preceded
by a line of Navigation Links:
The last, red marked item in this navigation list informs you on which page you currently are.
In this example it is the Gene Page for the gene mlcE. By clicking on the 'Chromosome' link
you navigate to the Genome
Browser.
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This section lists any names
and synonyms for a particular gene.
It also includes the Gene Product, a brief Description,
and the unique dictyBaseID for the Primary Feature, which, when curated, is the Curated Model.
- Gene Product
The Gene Product field lists the protein or gene product that the gene encodes.
- Description
The Description field provides additional information about a gene product.
- dictyBaseID
A unique identifier for each feature in dictyBase. Features generally correspond to sequences, and
a Primary Model is the best available sequence. In case a gene has been curated, the Primary Model corresponds
to the Curated Model.
A given gene can have more than one dictyBaseID: every GenBank record, Curated Model,
Sequencing Center Gene Prediction, and EST has a unique dictyBaseID (see also the Chromosomal Coordinates section.
While dictyBaseIDs always point to the same database entry, entries are sometimes deleted or
modified in such a way that they require a new dictyBaseID. The following are examples of this:
- Issues with Sequencing Center Gene Predictions: When gene models from Sequencing Centers change
it is possible that new dictyBaseIDs are generated and others are deleted.
- Issues with cloned genes: Some genes have been cloned by different groups and were given
different names, creating two different loci. Curators merge the two entries into a single gene page,
therefore deleting one of the dictyBaseIDs.
To help you find these dictyBaseIDs we have implemented a redirect feature: whenever possible,
searching for a defunct dictyBaseID will redirect you to the current one. An example is the K4 gene,
which was also called ksnD. We merged the two loci under the ksnD name.
Going to the K4
dictyBaseID DDB0003768
leads to a page that maps the new dictyBaseID: "DDB0003768 has been replaced by DDB0191404", with a link to the new page.
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This section contains location information, a chromosomal map, and, if curated, curator notes.
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This section contains a list of all features (sequences) associated to the gene
and their dictyBaseIds.
The IDs are all linked to their respective Sequence Info Page,
and to the left of each ID you'll find a link to the BLAST option on the Sequence Info Page.
To the right of each ID is a button providing a direct link to BLASTP at NCBI.
The Primary Model is highlighted in yellow.
Feature Types are indicative of the source of the sequence:
- Curated Model: Gene Predictions from Sequencing Centers are manually upgraded by dictyBase curators
if there is evidence that the gene exists. Such evidence includes GenBank records, ESTs, or high similarity to genes
known to be expressed.
Even if there is only partial evidence, such as high similarity of conserved domains only,
or limited EST coverage, a Curated Model is added with the extra label 'incomplete support'. Based on available data upgrading
may include the exon/intron
boundaries and/or the total length of the molecule. Currently the chromosomal sequence cannot be edited, only the
gene coordinates. This sometimes creates unsolvable situations, in which curators are forced to keep the Sequencing Center's
model. The evidence used by the curator to create the Curated Model can be found in Notes
- Gene Prediction from Sequencing Center: Gene models as provided by the Sequencing Centers.
- Genomic Fragment: The Genomic Fragment feature type corresponds to gene sequences in DNA GenBank records.
Note that it does not necessarily correspond to GenBank coding sequences.
- mRNA: The mRNA feature corresponds to the sequence provided on mRNA (cDNA) GenBank
records and may contain 5' UTR and 3'UTR sequence.
- EST: ESTs are expressed sequence tags, and are identified as such on their GenBank records.
These are considered partial cDNA sequences.
- contig: A stretch of genomic DNA assembled from raw sequence data. The contig lengths vary and may span part
of a gene or many genes. When enough overlapping contigs become available they are assembled into
whole chromosome sequences.
-
This section contains the length and molecular weight of the protein.
In the future, protein domains will be listed and displayed here. The link 'View
Sequence Information Page' leads to the protein section of
the Sequence Info Page.
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- Gene
Ontology (GO) Annotations: Molecular
Function, Biological
Process, and Cellular
Component
The GO annotations describe a gene's molecular functions, its role in biological
processes, and its presence in cellular components or complexes. The
GO annotations use a controlled vocabulary that will allow powerful searches
within dictyBase and across other databases. Each annotation
links to a page showing the term definition, a link to AmiGO, the Gene Ontology Browser, and all Dictyostelium
genes annotated to the term. For more information on all GO terms for a given gene click on the link 'View
Gene Ontology evidence and references' (see GO Help Page)
For more information about
the GO project, see www.geneontology.org.
-
this field contains links to expression data provided
by:
- The Baylor Functional Genomics team lead by Gad Shaulsky, John Halter and Adam Kuspa (micro array expression profile)
- Negin Iranfar, Danny Fuller, and William Loomis at UCSD (micro array expression profile)
- The Japanese Atlas database (in situ expression data)
.
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The Phenotype field lists the mutant phenotypes for the gene if available, along with details about
the type of mutation that produces the phenotype. Clicking on 'Phenotype details and references' leads
to a detailed list of phenotypes for the gene queried. Clicking on a specific phenotype opens a
referenced list of curated genes whose mutation(s) result in that phenotype.
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This field provides links to other information sources for the gene.
This includes the Researchers working on the gene; if there is more than one contact
person for a gene, this link retrieves a list of Colleague entries. Researchers listed must have
an entry in the dictyBase
Colleague database.
Other links include GenBank records,
Entrez Protein records,
and Uniprot records. More
information on these databases can be found in dictyBase's glossary.
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The Gene Summary Paragraph is a summary
of published biological information for a gene and its product that is designed to
familiarize both Dictyostelium and non-Dictyostelium researchers with the general
facts and important subtleties regarding a locus. dictyBase curators compose Gene
Summary Paragraphs
using natural language and a controlled vocabulary based on the Gene
Ontology (GO). Gene Summary Paragraphs contain links to references and GO terms
that will lead to PubMed or a page showing the term definition and all
Dictyostelium genes annotated to the term, respectively. These links are listed below:
- Links to references. Each fact presented in
a Gene Summary Paragraph is supported by one or more references. Clicking on a
reference goes to the appropriate dictyBase "curated paper" page.
The references with links to dictyBase "curated paper" and PubMed are also listed just
below the citation.
- Links to Locus Information for mentioned genes.
Any Dictyostelium gene other than the gene which the Gene Summary Paragraph is about
is linked to its dictybase Gene Page within the paragraph. Click on the gene
name to see its Locus information.
- Links to GO annotations.
Links to a page describing the GO term itself and a list of genes in dictyBase that
are associated with that term. For more information, go to
the GO Help Page.
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This section displays the 5 most recent publications that mention the gene
or its synonyms. Clicking on the
'View Literature Guide for complete listing of references'
link retrieves dictyBase's Literature Summary Page, which organizes papers about a gene
by various topics.
We greatly welcome general input from the
community regarding the annotations, as well as any
specific information we should incorporate into the summary for a particular
gene. Please send any suggestions to dictybase@northwestern.edu.
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