dictyBase Help: Gene Page



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.

  • 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.
  • 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)
    • .

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

Relevant dictyBase Glossary Terms

Home| Contact dictyBase| SOPs| Site Map  Supported by NIH (NIGMS and NHGRI)