Page History

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[Study Name]

When you log in, one study displays in the left sidebar by default. Any study that you select in the My Studies drop-down list in the upper right of the page replaces this default selection.

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Home

Click this to return to the home page for the selected study.

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Search [Study Name]

Click this option to open the Search [Study Name] page from which you can launch queries into your selected study. For more information, see [3 - Searching a caIntegrator Study].

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Study Data

Click Saved Queries > My Queries to open the list of previous queries you saved. Click any item in the list to open the saved query, which displays on the Criteria, Columns and Sorting tabs. From those tabs, you can modify criteria and/or launch the query again. For more information, see Saving a Query.
Click Saved Lists > Global Lists or > My Lists to open gene lists that have been saved for a study. From any page in caIntegrator that shows such a group, you can save a such a list of genes to be used for searches or analyses. See Creating a Gene or Subject List.
Click Saved Copy Number Analysis to open an Edit GISTIC Analysis page. You can review genes retrieved from the analysis or, with appropriate permissions, you can edit the metadata for the analysis. See Editing a GISTICAnalysis.

Analysis Tools

Click any of the listed options to open a page where you can launch an analysis of the data in the selected study.

• Generate a K-M Plot. See Creating Kaplan-Meier Plots.
  
• Generate a Gene Expression PlotsPlot. See Creating Gene Expression Plots.
  
• Launch GenePattern Analysis. See Analyzing Data with GenePattern

Study Management

Click either of the listed options to manage the selected study through editing or deleting it or by creating a new study.

• Click Manage Studies. See Managing a Study.
  
• Click Create a New Study. See Creating/Editing a Study.

Application Management

Click Manage Platforms to identify, add or remove platforms that caIntegrator supports. For more information, see Managing Platforms.

caIntegrator Menu

• Click Support to view contact information for Application Support.
  
• Click User Guide to open the caIntegrator v.1.3 User's Guide in wiki format.

Help

Click the Help icon at the top of each page to open a context-sensitive topic. The help page displays information (from this user's guide) that corresponds to the page from which help was opened.