Newsletter 4 (Jul 2008)

Release Date: 
July, 2008
Download newsletter: 
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News: 
  • Taxonomic change
    NCBI have changed the taxonomic name for Culex pipiens quinquefasciatus to simply Culex quinquefasciatus. Over the coming months VectorBase will be making this change on the website in line with the GenBank entries. The taxon identifier remains unchanged (7176).
    Data: 
    • Gene set update
      Manual appraisal of a subset of the initial Culex gene set has been undertaken and we were able to identify approximately 1,500 genes that appear to be mis-predicted. These predictions have been removed from the canonical gene set. The majority of the deleted genes were short (1 or 2 exons) and lacked clear orthologs with other species (both the mosquitoes and beyond) but had many paralogs within Culex.

      The new gene set, CpipiJ1.2, is available at VectorBase and has been submitted to GenBank. A list of the deleted genes is available on our website.

      We value input from the community; so if you spot a gene that you think should be deleted or corrected, please e-mail us and we will incorporate it into the next update.

    • Expression data resource

      The VectorBase gene expression resource (VBGE) continues to develop with a new user interface that makes finding and browsing experiments far easier and allows for the integration of Affymetrix data for the first time.
      A number of new data sets have been incorporated for Anopheles gambiae dealing with expression changes during blood meals and expression in adult tissue and larval gut compartments.
      You can access the data through the VBGE2.0 website by searching using gene or reporter names, and experiment descriptions. Links to expression summaries are available through the web browser, via the left hand navigation menu of a Gene Report page (see below).

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    Top tip: 

    Did you know you could add a comment to a gene?
    From the Gene Report page, in the Gene DAS Report section, click on “Add a comment”. You will need to have a VectorBase user account (so that comments and annotation submissions can be properly accredited). If you don’t already have an account, just sign up - it only takes a couple of minutes. Your comment will appear in the Gene DAS Report section.

    You can also use this system to associate gene descriptions, Gene Ontology terms and literature citations

    Updated on February 2014: This was only possible with the old (or classic) VectorBase.