Transcriptomics Experiment and Comparison List


Transcriptomics Experiment and Comparison Lists Overview

For any taxonomy level or genome, all publically available transcriptomics experiment datasets that are incorporated into PATRIC are displayed as Experiment and Comparison lists.  The Experiment Tab shows a list of studies or datasets that contain one or more samples or experimental conditions.  The Comparison Tab shows a list of curated pair-wise comparisons of two samples or experimental conditions to provide differential gene expression measurements.  Metadata-based searching and progressive filtering allows you to quickly find datasets of interest.


Accessing Transcriptomics Experiment and Condition Lists

Experiment and Comparison lists can be accessed via the Transcriptomics tab on any Taxonomy or Genome level landing page.


Using Transcriptomics Experiment and Condition Lists

  • All tables accessed via the Experiments and Comparisons Tabs may be sorted as described in Feature Table FAQs.
  • Filter controls on the left allow you to filter the data based on the following key metadata attributes (in orange text):  Sample Organism, Strain, Gene modification, Experimental condition, Time series, and Release date.  To see all of the information associated with a specific attribute in the list, click the “more” buttons, located within the list.
  • From the Experiments tab, using links provided in a row, you can navigate to an individual experiment landing page (Title), Gene List (Genes), publication page at NCBI PubMed (PubMed), or detailed experiment page at NCBI’s GEO database (Link Out).
  • From the Comparisons tab, using links provided in a row, you can navigate to corresponding Gene List (Genes), list of significant genes based on log ratio (|Log Ratio| >= 1), list of significant genes based on Z-score (|Z-score| >=2), publication page at NCBI PubMed (PubMed), or detailed experiment page at NCBI GEO database (Link Out).
  • From either tab, you can use the Table Toolbar, located in the light blue row to:
    • Select one or more Experiments or Comparisons of interest and save them to your workspace as a group by clicking the toolbar_icon_add features Add Experiments button.  Creating a group from the Comparisons tab will add the entire Experiment to your workspace.
      • Note: If you are a registered PATRIC user and logged in, your Experiment group(s) will be permanently saved to your workspace.  To learn more about the benefits of registration, and how to save data for future visits and utilize your personal workspace, see Registration FAQs and Workspace FAQs.
    • Select one or more Experiments or Comparisons and create a Gene List.
    • Download selected Experiment data in both excel and txt file formats.
    • Customize which metadata columns are shown/hidden in your results table with the toolbar_icon_hideshow_column Columns button.
    • Access the PATRIC FAQs glossary within PATRIC eNews by clicking on the toolbar_faq icon PATRIC FAQs button.