Sets are a convenient way to perform searches and save lists of relevant genes or experiments. Some experiment sets are built into Gemma (such as the sets that list all experiments for each taxon and the sets that hold taxon subsets, for example, one set lists all the human experiments in Gemma that have to do with the brain).
Each set can only hold elements from one taxon and sets cannot be empty.
Sets can be public, private, or shared.
A public set can be seen by all Gemma users, even those who are not logged in.
A private set can be seen only by its owner and administrators.
A shared set is a private set that the owner has deliberately shared with other sets of registered users. Go to “My Gemma”->”User Groups” to make a group of users, then click on a set’s “lock” icon (which indicates a private group) to edit who it is shared with.
Making and Editing Sets
There are many ways to make sets in Gemma, however you can only do so if you have created a user account and are logged in.
- Gene set manager: In the top menu, go to “My Gemma”->”Gene Groups”. In the left panel, you will see a list of all your gene sets (if any exist). To create a new set, click the “+” button at the top left. After entering a name and description, you can add genes to your set using the panel on the right. Be sure to press the save button at the top left when you’re done building your set.
- Experiment set manager: In the top menu, go to “My Gemma”->”Experiment Groups”. In the far left panel, you will see a list of existing experiment sets, both public and private. To create a new set, click the “+” button at the top right. After entering a name and description, you can add experiments to your set using the middle panel: first find experiments using the search box, then use the “Grab >>” and “Grab All” buttons to add selected experiments to your set. To see details for any experiment, select the experiment row and look at the bottom panel.
- Search form: From the search form on the front page or in the analysis search page (“Explore” -> “Search Analyses”), you can save sets before or after you use them for a search. After you’ve built your gene or experiment selections (see the “Setting up the query” section of this guide), you can edit them and save them using the icon in top right of the preview window (figure 2, box A). This will bring up a window where you can add and remove elements from your set. Click the “Save” button to either save over an existing set or save a copy of your new set (you will be given the choice).
- Differential expression visualiser: Select genes and conditions by holding down the “Ctrl” key and clicking on row and column headers. You can save your selections as gene and experiment sets in Gemma using the “Save Selected” button in the top toolbar. You can also get a text version of your selections by pressing this button and then clicking on “Export” in the window that pops up.
Sets that are built using the search form but are not explicitly saved will be stored temporarily, for convenience. You may have three temporary sets at any time and the oldest will be replaced when a fourth is created. If you wish to save a temporary set, click the save/edit button in the top right of the preview window (figure 2, box A). You will be prompted to log in or register.