Manage gene sets

What are gene sets and what can I do in here? Gene set refers to groups or lists of genes. This set can consist of a couple of genes or hundreds of genes. This allows you to group genes into convenient collections for reuse. You can group a few genes for quick search retrieval or for use in a cohort query. In this tab, you can create, edit, and manage gene sets.

A few things to keep in mind about gene sets in Oracle Healthcare Translational Research:

• There are no restrictions on genes that can be included in a gene set. You can mix genes from multiple species or assembly versions.
• The same gene can be part of many different gene sets.
• Gene sets are private and cannot be shared among users.
• Gene set names are not case-sensitive.
• When genes are compared using the Contains or Starts With option, the limit is 512 characters.

For more information, see:

• Create a new gene set
  
• Edit a gene set
  
• Manage a gene set
  

Create a new gene set

1. Along the top, click Manage Gene Sets and go to the Create New or Edit section.
2. Specify the genes you want to include in the gene set. This can be done in three ways:
   • Type in Gene Names - Search for genes using their Ensembl or HUGO names. You can enter multiple gene names separated by space, comma or semicolon.
   • Add from existing gene set - Search for genes based on an existing gene set.
   • Upload from a file - Select a text file (CSV, TSV, TXT) from your computer where the genes are delimited by comma, space or tab. Click Choose File to browse for the file.

   Note:

   The file size limit is less than 5MB when genes are matched using Equals.
3. Select a value for Species.
4. Select an Assembly Version.
5. Click Submit. The matching genes appear in the Available Genes pane.
6. Use the arrow () to move available genes to the Final Gene Set panel.

   Use the double arrow () to move all available genes to the Final Gene Set panel.

   To remove genes from the Final Gene Set panel, use the Remove or Remove All buttons.

7. In the Save Gene Set section, enter the name and description of the gene set.
8. Click Submit.

Edit a gene set

To edit a gene set:

1. Along the top, click the Manage Gene Sets tab, and go to the Create New or Edit section.
2. Search for the gene set you want to edit using the Add from existing Gene Set option.
3. Select a value for Species.
4. Select an Assembly Version.
5. Click Submit. The gene set appears in the Available Genes pane.
6. Use the arrow() to move available genes to the Final Gene Set panel.

   Use the double arrow () to move all available genes to the Final Gene Set panel.

   To remove genes, use the Remove or Remove All buttons.

7. Click Submit.

Note:

When you search genes using the Contains or Starts With option, the limit is 512 characters

Manage a gene set

To manage a gene set:

1. Click the Manage Gene Sets tab and go to the Manage section.
2. Enter the gene set you want to modify.
3. Click Submit.

   To print the data, click Print on the top right.

   To export the data in an.xls file, click Export.

   To remove a gene set, click Delete Gene Set at the bottom.

   Note:

   When you delete a gene set, its record is still available in the database but it can only be restored by a system administrator.