Table of Contents

Interacting with Sungear

Selecting

Almost all dialogs in Sungear allow the selection of elements or groups of elements. Selected elements will often highlight or affect values seen across all the dialogs.
For Mac users:
Alt = Options/Alt key
Ctrl = Apple Key

Basic
Left Click : select an item in a list, or a vessel or anchor inside the sungear dialog.
Shift Left Click : select a range of items in a list. L-Click the first item of the range then Shift L-Click on the final item to select the range.
Advanced
Once the basics of selecting have been mastered there are two additional types of selection in Sungear that allow more control over the data.
Ctrl Left Click : Unions an anchor/vessel/term with a previous selection. From then on, toggles between selecting all or none of the genes in the anchor/vessel/term.
Ctrl Alt Left Click : Starts a multiple select for union and intersection. Performing this action will highlight the Union and the Intersection buttons in the control dialog. Once elements have been selected pressing the Union or Intersection button finishes the command.

Control Dialog


What you are seeing

The general management tool for sungear data.
Restart : reloads data set
All : select all groupings
None : select no groupings
<< : Go backward to a previous selection
>> : Go forward to a selection
Narrow : Create a new group based on selected elements and clears selection history.
Union : Union two or more selected elements. Select multiple elements using Ctrl-Alt L-Click, then click Union.
Intersect : Intersect two or more selected elements. Select multiple elements using Ctrl-Alt L-Click, then click Intersect.
Find Cool : Find the vessel consisting of the most overrepresented set. The results are saved after the first click. If saved results are available, the button will read "Show Cool".
Export : Export data set
View Group : View this group

Genes Dialog


What you are seeing

The main part of the genes dialog is the Table that contains ID and Description. This gives you the gene ID and the description. Selecting a gene from this list will highlight associated vessels in the Visualization dialog. Also selections made from the Visualizations dialog will highlight the corresponding genes in the genes dialog.
The numbers in the lower left corner represent the number of genes selected and the total number of genes in the current group, chosen by a narrow or a view group operation, just like at the lower right of the sungear dialog.

GO Terms Dialog


What you are seeing

The upper window shows the GO Terms, in heirarchal fashion, that can be selected.
The bottom window shows the GO Terms in list fashion sorted by z-score.
The bar to the left is a visual representation of the number of selected genes for that term, relative to the total number of genes for that term in the current group. The number on the left is the z-score. The number on the right is the total number of genes for that term.

Sungear Dialog


What you are seeing.

Anchors are the names you see circling the display. Vessels are in the center. The number in the upper right hand corner is the number of selected genes in the current highlighted vessels/anchors. The numbers in the lower right hand corner are the number of genes selected and the total number of genes respectively. In the lower left hand corner are arrows that allow you to move backwards and forwards through anchors.

Definitions

Anchors : A list of genes corresponding to some outcome of an experiment(e.g. the induced genes). Anchor terms can be seen surrounding the visualization circle in the sungear dialog.
Vessel : List of genes in the intersection of the anchors to which that vessel points and that are not in the intersection of any superset of those anchors. Selecting a vessel highlights the genes in the Genes Dialog as well as all anchors associated. Size depends on the ratio of genes found inside the vessel compared to the total number of genes in the last created group.
GO Terms : Gene Ontology Terms, Name for genes that participate in particular functions

Troubleshooting

I just see a gray screen?

If you have arrived on the sungear page with only a gray screen to greet you it is most likely a Java problem. Most likely either Java is not installed or the Java version is an older version not supported by Sungear. Sungear is known to work whttp://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmedith Java versions 1.5.0+. Java can be downloaded from the Sun website. You can test to see if you have Java and what version you have here. Java Version Test

I upload a file but nothing happens (the Sungear plot is empty)?

If you have tried this more than once and your data doesn't appear in Sungear after you upload (the sungear plot is an empty circle), then most likely this is a java version problem. If you update your java version to 1.5.0+ this should go away. Java can be downloaded from the Sun website. You can test to see if you have Java and what version you have here. Java Version Test

I am having problems with multiple selections?

If you are having problems with multiple selections and have tried using the Ctrl L-Click and Ctrl Alt L-Click then please contact us. For Mac users sometimes releasing the apple key for a second then repressing it will allow selections on different windows.

I get Out of Memory errors?

Some Sungear files need more memory than the browser usually allows for Java. In order to load these files, you need to increase the amount of memory that Java can use by following these steps:
  1. Run the Java Plugin Control Panel
  2. Click on "Advanced" (or, on a Mac, the "General" tab), and in the space provided under "Java Runtime Parameters" type the following string exactly as shown:

    -Xmx256m

    Now click "Apply" ("Apply Now" on a Mac). This will increase the available memory for Java to 256MB. If you still run out of memory, you can change the number after the -Xmx to something larger, but be sure not to forget the "m" after the number.

  3. Close all open browser windows. When you open the browser again, Java will be able to use more memory.

I get a "no genes in data set" error when I upload my data?

This means that Sungear doesn't have any information about the genes in your experiment. Usually this means that you've picked the wrong species from the pull-down list. It may also means that Sungear doesn't have information on your species, or your gene IDs are different from the ones that sungear knows about. If you need to have another species or set of gene annotations added to Sungear, write an email to the Contact Us address on the demo page.