Home

1. Introduction
2. Interacting with Sungear
3. Control Dialog
4. Genes Dialog
5. GO Terms Dialog
6. Sungear Dialog
7. GeneLights Dialog (optional)

Interfacing with Sungear from third-party applications

1. Data exchange using a web application

Introduction

Sungear enables rapid, visually interactive exploration of large sets of genomic data. It allows browsing of gene sets by experiment membership, gene annotation, and ontological term. The purpose of Sungear is to make otherwise complicated queries quick and visually intuitive.

Authors

• Radhika Mattoo
• Dennis McDaid

Quick Links

To start Sungear with one of our pre-loaded data files, click the corresponding link below. After launching Sungear, you can switch to a different pre-loaded data set using the Sungear menu option File | Load...

• Microarray data: This dataset was generated from published microarray studies that identified Arabidopsis genes regulated by transient treatments with the nutrients nitrogen (N) and or carbon (C) (Price, J., et al. (2004) Plant Cell 16, 2128-2150; Scheible, W.-R., et al. (2004) Plant Physiol. 136, 2483-2499; Wang, R., et al. (2004) Plant Physiol 136, 2512-2522. ). In this example, six lists of genes containing N- or CN-regulated genes (I= induced; D= depressed) provide the anchors for Sungear. These experiments conducted by three different research groups all share the feature of transiently treating Arabidopsis seedlings with nitrogen or nitrogen plus carbon nutrients, and assaying gene responses using the ATH1 Affymetrix whole genome chips.

• Comparative Genomics: This dataset was generated from a BLASTP comparison of all Arabidopsis thaliana protein sequences to the protein sequences in C. elegans (worm), D. melanogaster (fly), H. sapiens (human), M. musculus (mouse), R. norvegicus (rat), S. cerevisiae (yeast), S. pombe (fission yeast), and a collection of Cyanobacterial, Archaea and bacterial genomes, as described previously (Gutiérrez et al. 2004). In this analysis, the Arabidopsis proteins are the "background" used for annotation (Gene names and GO terms).

• Developmental Time Course: Microarray Experiments from different developmental time points of Arabidopsis thaliana ( Shmid et al 2005 ) were grouped into different developmental stages (Seedling, Young Plants, Mature Plants, Flowering Plants, and Seed Development). Genes that were determined to be differentially expressed (using inhouse statistical analysis) were plotted using Sungear.

Upload Your Own Data

To view your own data in sungear, please interface with VirtualPlant's Gene Upload program which will be available soon here

Species refers to the source of gene annotations for the genes in your experiment. Pick the appropriate species from the pull-down list. If you don't see the species you need, contact us.

Experiment File is the file containing your data. Click the "Browse" button to choose a data file from your computer.

File format is the format of your data file. Examples of the acceptable data file formats are provided below.

Acceptable data formats

• FASTA-like format:

>List1
At1g01050
At1g01450
At1g01460
At1g01510
At1g01560
At1g01740
At1g02970
At1g03030
At1g03450
At1g03590
At1g03740
At1g03920
>List2
At1g03740
At1g03920
At1g77760
At5g53460
At1g05250
At3g49960
At5g17820

• Sungear data format:

List1 | List2 | gene
1     | 0     | At1g01050
1     | 0     | At1g01450
1     | 0     | At1g01460
1     | 0     | At1g01510
1     | 0     | At1g01560
1     | 0     | At1g01740
1     | 0     | At1g02970
1     | 0     | At1g03030
1     | 0     | At1g03450
1     | 0     | At1g03590
0     | 1     | At1g77760
0     | 1     | At5g53460
0     | 1     | At1g05250
0     | 1     | At3g49960
0     | 1     | At5g17820
1     | 1     | At1g03740
1     | 1     | At1g03920

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. Left Click the first item of the range then Shift Left 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 left-click, then click Union.
• Intersect : Intersect two or more selected elements. Select multiple elements using ctrl-alt left-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 Visualizations 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 hierarchal 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 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.

GeneLights Dialog

What you are seeing

Some experiments provide extra data to enable the GeneLights window, which can be opened by navigating to View | GeneLights. Given a value for each gene and experiment, GeneLights displays the distribution values for each experiment as a histogram shown above. Typical biological values are gene expression, or a function thereof such as the (log) fold change in expression. When the user selects a set of genes in another window, GeneLights highlights that set in the histogram, leaving the full set genes visible in a shadow histogram (similar to how selection of some genes in a vessel is show in the Sungear window).

Clicking on a bar in a histogram in the GeneLights window selects the genes with that value. ctrl-click on additional bars in any histogram will select additional sets of genes. Clicking and dragging on a histogram will select genes in that range for that experiment, and clicking and draggin in the top area selects genes in that range across all experiments.