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GemScape

Introduction

GemScape 1.0 is a plugin for Cytoscape that allows you to visualize and interact with Gemma’s coexpression data. The Gemma web site gives you a lot more detail about the coexpression patterns than GemScape, but the power of Cytoscape is what you get in return.

This user manual assumes you know how to use Cytoscape and already have it installed. If not, visit Cytoscape.org.

Credits

GemScape 0.1 was written by Adam Hall (really 1.0-alpha). Additional coding was done by Paul Pavlidis.

Download

Click here: GemScape.jar and save the file to disk. Compatible with Cytoscape 2 or earlier.

Install

Copy GemScape.jar to your Cytoscape plugin directory. Under Windows, this might be “C:\Program Files\Cytoscape 2.6\plugins”.

When you first start Cytoscape, you should see the “GemScape” tab at the left of the screen. If not, check the error logs and report any messages you see in the “warnings” tab. We’ve tested it with Cytoscape 2.6.1.

User guide

Quick overview

A typical GemScape use case would be as follows:

  • Choose one or a few genes to seed your network.
  • Get results to create an initial visualization
  • Examine the resulting network, adding queries interactively to expand it.

You can view some details about the nodes (genes) and edges (coexpression results), and of course do anything else that Cytoscape.

What you need to start is the official symbol of one or more genes from a supported taxon (currently mouse, human and rat). The official symbol of a gene is often different from the common name. For example, GRIN1 is the official symbol of what many people call NR1. We get our official symbol information through NCBI.

Walkthrough

Click on the thumbnails to view the screenshots.

Main panel

Here is what the user interface looks like at first, after typing in the symbol for one gene.

To start off, use the following steps:

  1. Confirm that GemScape was able to connect to Gemma’s server.
  2. Choose a taxon
  3. Use the “add query genes” field to enter gene symbols to search. You can enter more than one, one per line.
  4. Click the “add query button”. The genes you entered should show up in the table at the left. If not (or if some are missing), check that you have the right symbols. GemScape only understands official gene symbols.
  5. Use the “Select scope” pulldown to choose which data sets to search.
  6. If you entered more than one gene and only want to find coexpression among those genes, click “My genes only”.
  7. Click “Create new network”. It takes a few seconds (usually) for GemScape to get results from the Gemma server.

Optional settings

  • Select stringency: How strong does the coexpression have to be before it is shown? Values must be at least 2, but we recommend setting this higher (~10) to start with, and lower it if you don’t get many results back. The exact lower limit you use will depend somewhat on how many data sets are being searched (the “scope”). Large scopes work better with larger stringencies. Note If “auto-choose stringency” is checked, GemScape may adjust the stringency to a higher value to keep you from getting too many results.
  • Max coexpressed with each gene: You may increase or decrease this to change the limits on how many results you will get per gene. Note that GemScape has an upper limit anyway, so setting this very high won’t do anything. A value of 20-50 seems sensible.

Advanced settings

  • Specific probes only: If you uncheck this, results from expression assay probes which “hit” more than one gene will be allowed. We recommend keeping this checked, to avoid getting a lot of questionable results. There is a tradeoff here as you might miss some legitimate results.
  • Auto-choose stringency: If you uncheck this, the exact stringency you set will be used, which can sometimes end up with too many results. If checked, GemScape will choose a stringency that keeps the results from hitting the “max coexpressed” limit. We find that leaving it checked helps keep the networks from getting out of control.

After a search, here is what it might look like

Adding more searches

Currently, the only way to add to a GemScape network is to use a contextual menu. Select some genes, and then right-click (Mac: option-click) on a gene, and look for the “Gemma” submenu (I couldn’t get a screenshot of this).

There are two choices:

  • “Make the selected node(s) queries” – The selected genes are sent back to Gemma to get their coexpressed genes, using the settings on the main panel. They are added to the network.
  • “Complete network for selected nodes” – To “complete” a network means to check for coexpression among all the selected genes. This is necessary because by default, GemScape only returns coexpression links between your queries and other genes. If the “other” genes are also coexpressed, that will not be shown until you use the “complete” function. This option only works if you have selected at least two nodes.

Here is what it looks like after we added one more query to the network.

Here is what it looks like after completing the network.

Viewing node and edge attributes

If you are familiar with Cytoscape, you know about the “Data panel” at the bottom of the window. If you click on the “Select attributes” icon, you can select several attributes of GemScape nodes and edges including:

Nodes:

  • Gene symbol
  • Gene name
  • NCBI ID

Edges:

  • + or – for positive and negative correlations respectively
  • Support value: how many independent expression studies found the coexpression.

Gene attribute view, see bottom of screen:

Edge attribute view, see bottom of screen:

Note that the attributes shown in the table are not displayed by default. You must click on the “Select attributes” icon in the Data Panel. We haven’t figured out a way to make them show up by default.

Troubleshooting

You should see “connected” at the top of the page, as in the screenshot. If not, make sure you have a valid internet connection and your firewall isn’t interfering. If that’s not the problem, let us know right away!

Limitations

We have put some limits in place to keep users from swamping our servers with requests.

  • Gemma will return at most 100 results for any query. The most significant results are returned.
  • You can only send queries for a certain number of genes at once, currently this is set to 100.

Contacting us about GemScape

Requesting new features

GemScape is fairly bare-bones. We are happy to consider feature requests. Please email gemma@chibi.ubc.ca.

Reporting problems and bugs

Please email gemma@chibi.ubc.ca with the following information:

  • Operating system (e.g., Windows 8) and version.
  • Cytoscape version
  • If possible, the text in the error console when you had the problem, especially any “warnings”. The Cytoscape error console is viewable through the “help” menu, “error console” item.
  • A brief description of what you did to reproduce the error.