VBGE feature requests

The following features have been suggested/requested to enhance VectorBase Gene Expression. Please contact us if you have other ideas. Thanks in advance!

  • Search on expression, e.g. "upregulated in pupa"
    • coming in VB1.1
  • Checkbox list selection of experiments to be included in expression summary (especially when there are more experiments)
  • Allow the user to change sort order of expression summary table
  • Allow the user to change the plot order
  • Some kind of automatic indication of "bad" reporters (that don't agree with other reporters for a given gene)
  • More sophisticated statistical treatment of technical replicates
  • Show expression summaries for a list of genes
  • Clustering of genes based on their expression (across all experiments, if possible)
  • Add experimental factor icons to Experiment list and individual pages
  • Provide search/experiment/microarray list view sort options.
    • also add search filter
    • provide clearer indication of species for each experiment
    • provide information about number of hybs (for experiment) and biological/technical replicates (for biological replicates, count how many unique samples or sample pairs there are)
      • planned for 2.2
  • Provide "next/previous" experiment (and perhaps gene/reporter) navigation links or menus in the reporter-experiment pages (these are the pages with the plots)
  • Checkbox selection of reporters next to the "unaveraged plots" with a submit button to take the user to a custom multiple reporter page, e.g. like this, see also [1] as an example where it would be useful
  • Linking to/from CV/Ontology browser (via terms like "midgut", "ovaries", "permethrin")
  • remove SeriesLabel and SeriesIndex annotations from all samples
  • deal with no data for reporter nicely
  • expression plots should have a more accurate y-axis label (discriminating between "ratio" or "expression level", depending on the platform)
  • display more gene information - not as easy as it sounds, unfortunately.
  • random gene+experiment plot on main page?
  • arrange for methodical indexing by Google if such a thing is possible.
  • Use full species name Plasmodium berghei in experiment names (and configure relevant URL redirections)
    • fixed on 2008-10-15 (Apache is redirecting P. berghei to Plasmodium berghei for continuity)
  • on experiment and microarray pages, provide relevant search tips for the reporter search
    • probably implemented through annotating the array design with an "example reporter" annotation (VBMicroarray class reqd)
    • planned for VBGE2.3
  • be more integrated with rest of VB - all linked gene IDs should go to the genome browser gene page (not to an expression page as currently)