dictyBase Help: Gene Page

Contents

• Description
• Content of the Gene Page
• General Information
• Chromosomal Coordinates
• Associated Sequences
• Sequence Types
• Regulatory Elements
• Protein Information
• Gene Ontology Annotations
• Expression
• Strains and Phenotypes
• Links
• Summary
• Latest References
• Relevant dictyBase Help Documents
• Relevant dictyBase Glossary Terms

Description

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.

Content of the Gene Page

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.

• General Information

This section lists any names and synonyms for a particular gene. It also includes the Gene Product, a brief Description, and the unique Gene Identifier.

• Gene Name
  This is the primary gene name, preferably used when referring to a gene in publications.
• Synonyms
  These are gene or protein names that have either been published or that add a common name for comparative studies.
• Gene ID
  This is the primary, unique identifier for each gene in dictyBase. This Gene ID has the format DDB_G####### (for example, DDB_G1234567) and is stable regardless of curation status of the gene.
  
• 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.

• Chromosomal Coordinates

This section contains location information, a chromosomal map, and, if curated, curator notes and icons for easy recognition of the curation status.

• Location
  This field provides information about gene's location: the chromosome and strand, and the chromosomal coordinates.
• Genome Browser Snapshot
  This section shows a snapshot of the gene model in the Genome Browser. From the color of the gene model, the gene's orientation and curation status can be recognized. In a red gene model its open reading frame is oriented on the top DNA strand (Watson), while a blue gene model is on the bottom strand (Crick). A dark red or blue shows that the gene model has been manually reviewed by a dictyBase curator, whereas a light red or blue gene model indicates that the gene model has not yet been curated. Clicking anywhere on the map will link to the actual Genome Browser page.
• Notes: When a gene has been curated, a note by the curator describes the evidence used for the gene model to be confirmed. The evidence can be "gene sequence", "mRNA", or "ESTs", or "Sequence Similarity". Notes may also alert the user to specific information about the sequence or gene model.

• Associated Sequences

This section contains a list of all sequences associated to the gene and their dictyBase Ids, DDB#######, (e.g. DDB0123456). Sometimes sequence IDs expire, e.g. when a sequence changes. However, we have implemented a redirect feature that leads to the updated dictyBase ID. 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 the Gene Model feature is a button providing a direct link to BLASTP at NCBI.

Sequence Types are indicative of their source:

• Gene Model: The primary Gene Model is highlighted in yellow. This is the best available gene model, either a manually reviewed gene model or a gene prediction from the Sequencing Center. The curation status is indicated by an icon:
  This green icon is only present if a gene model has been manually reviewed by a dictyBase curator. Based on available data, verifying a gene model may include updating the exon/intron boundaries and/or the total length of the molecule. If there is only partial evidence for a reviewed gene model, such as similarity to conserved domains only or limited EST coverage, the note 'incomplete support' has been added. This is indicated by a question mark:
  Currently the chromosomal sequence cannot be edited, only the gene coordinates. This sometimes creates difficult situations, e.g. when several ESTs agree but the genomic sequence has an insertion, deletion or changed nucleotide. Curators then create artificial small introns, or create a gene model that does not have a start or a stop codon, to produce the best possible gene model. These gene models are marked 'conflicting evidence', and by an exclamation mark:


• GenBank Genomic Fragment: These IDs link to Genomic Fragment sequences, which correspond to gene sequences in DNA GenBank records. Note that it does not necessarily correspond to GenBank coding sequences.


• GenBank mRNA: These IDs link to mRNA sequences, which corresponds to the mRNA (cDNA) provided by GenBank that 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.

• Regulatory Elements

  This section represents putative transcription factor binding sites predicted as described in dictyBase - a Dictyostelium bioinformatics resource update. Fey, Gaudet, Curk, Zupan, Just, Basu, Merchant, Bushmanova, Shaulsky, Kibbe, and Chisholm. Nucleic Acids Res, database issue, 2009. Clicking on the dictyBase ID leads to a new page with detailed information on gene expression for that gene and a graphical overview of the promoter structure.

• Protein Information

This section contains the length and molecular weight of the protein as well as a display of protein domains. The link 'View Sequence Information Page' leads to the protein section of the Sequence Info Page.
The protein domain display includes popup ballons with domain names and coordinates that are clickable with links to source databases. The link to 'Table view' displays a list of associated domains as in this example.

• Gene Ontology Annotations

  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.

• Expression

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)
.

• Strains and Phenotypes

This section lists the strains in which the gene has been mutated. Strains are listed by Strain Descriptor, which summarizes the mutation in the gene. To the right of the strains, mutatant phenotypes are listed. Clicking on a specific phenotype opens a referenced list of curated genes whose mutation(s) result in that phenotype. Clicking on the strain descriptor leads to a separate Phenotype and Strain Details Page where all phenotypes are listed with references and additional information such as assay and environment used. Located below the list of phenotypes is detailed strain information including strain names(s), genotype, mutagenesis methodsa link to the original publication, and a link back to the gene page. See an example of a Phenotype and Strain Details Page.

• Links

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.

• Summary

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:

1. 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.

2. Links to Gene 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 information.

3. 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.

• Latest References

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.

Relevant dictyBase Help Documents

• BLAST
• Literature Guide
• Genome Browser
• Gene Ontology (GO)
• Sequence Page

Relevant dictyBase Glossary Terms

• Curated Model
• EST
• Gene Name
• Standard Name
• Synonym
• GenBank
• Gene Ontology (GO)
  • Molecular Function
  • Biological Process
  • Cellular Component
• Description
• Gene Product
• Phenotype
• Uniprot
• Entrez
• Kyoto
• PubMed
• Gene Summary Paragraphs
• BLAST
• Colleagues