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MeV and Gaggle
MeV has supported the Gaggle framework since September 2008 (MeV v4.2). Gaggle is a powerful communications system that allows connects supported programs (geese) to seamlessly transmit data to one another, without the need for intermediate flat files. MeV can use the Gaggle to send and receive data with other systems biology platforms, such as R, Cytoscape, and various web databases.
To start using the Gaggle, you need to connect to the framework. To do this, simply select the Utilities -> Gaggle -> Connect to Gaggle menu at the top of any Multiple Array Viewer (MAV) window. A Gaggle Boss will launch, and the MAV window you used will connect to it. (The Boss may be minimized when it starts.) You should be able to see the Multiple Array Viewer window listed in the Boss window as one of the "listening" Geese. As you launch other Gaggle-enabled programs or open more Multiple Array Viewer windows, you will see them listed here.
You can see whether MeV is connected correctly with a quick test. Open a result viewer from one of MeV's many analysis modules, say, KMC. Choose a cluster, open an Experiment Viewer window (the one with a heatmap) and right click. Choose the menu option Broadcast Namelist to Gaggle. Now look open the Boss window and choose the tab marked Clipboard. You should see a list of the genes that were displayed in the MeV result window. Note that if you have more than one annotation type loaded into MEV, the annotation type that will be broadcast to the Gaggle will be the one currently displayed in the viewer. You can change the displayed annotation type with the Display -> Gene/Row Labels menu option.
MeV will allow broadcasts out of many of its viewers, including the Excel-like Table Viewer, the Expression Graphs and the Centroid Graphs. The Cluster Managers also allow broadcasting. Just click to select the cluster or clusters you want, and right-click to pull up the popup menu with the Gaggle broadcasting options. You can also broadcast data from the viewers in the bottom half of the Cluster Manager.
Transferring gene lists between Multiple Array Viewers
Each Multiple Array Viewer window is treated as a separate program by the Gaggle Boss. This means that different Multiple Array Viewer windows can broadcast data to each other via the Gaggle. This is an excellent way to move genelists between MAVs.* To do this, launch another Multiple Array Viewer window with the File -> New Multiple Array Viewer menu option in the small, skinny window at the top of your screen. Load a dataset in this window (for the purposes of this tutorial, choose the same dataset that was loaded into the first window). If you look at the Gaggle Boss, you will see that two Multiple Array Viewers are listed in the Gaggle tab. The second Viewer window automatically connected to the Boss, since the first one was already connected.
In the second MAV, a new window will appear, asking you what type of annotation is contained in the incoming broadcast. Choose the correct one from the drop-down menu, and MeV will search through the list of annotations of that type. It will choose only the exact matches, and present a list of those matching genes in another table. You can inspect the results of the match here, and choose whether to store the resulting matches as a cluster.
*It is not recommended to use Gaggle broadcasts to move expression data (matrices) between MAVs. Each Gaggle matrix broadcast can contain only one annotation value per row (gene) in the matrix, whereas MeV may have many different annotation values loaded for each one. MeV provides a method for creating a new MAV and populating it with a complete set of data from a viewer. This method is called Launch New Session and is found in the right-click menu of most viewers. In the Cluster Manager, it is in the popup menu under Open/Launch -> Launch MeV Session.
Firegoose and Web Resources
MeV communicates with online resources through a Firefox plugin named Firegoose. This plugin can be used to send lists of gene names to websites such as DAVID, EGRIN, EMBL String, Entrez Gene, Entrez Protein, Gaggle Web Applications, Halo Annotations, KEGG Pathway database and others. Here we will focus on DAVID and Entrez Gene. You will need to install Firegoose and restart your browser to follow along with this part of the tutorial.
Firegoose does not automatically connect to the Gaggle. To connect, go to the Firegoose toolbar in your web browser an choose GAGGLE -> Connect to Gaggle. In the Gaggle Boss window, both Multiple Array Viewer and Firegoose should be listed as "listening."
DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a useful tool for identifying enriched biological themes, finding enriched fun4ctional-related gene groups, clustering annotation terms, visualizing pathways, and more. (See the DAVID website for more details.)
Choose a list of genes to broadcast to the DAVID website. DAVID accepts the following annotation provided by RESOURCERER: AffyID, Refseq Accession, Genbank Accession, ENTREZ ID, Gene Symbol, Unigene ID. After broadcasting from MeV, you should see the Firegoose toolbar change to show a dataset name in the drop-down menu. Your list of genes is now in Firegoose. In the Target drop-down menu to the right, choose DAVID. The David website should load into your browser window. Now click the Broadcast button. Firegoose will load the list of genes into the DAVID input panel. A new tab will appear with the gene list on the right. Select the Identifier type of the gene list (the gene/row names being viewed in MeV), then click "Submit List."
Entrez Gene is NCBI's database of genes, found here. It provides a gene sumary, genomic regions, transcripts, and products, genomic context, a bibliography, interactions, GO terms, protein information, reference assembly etc. Entrez Gene only accepts 100 genes at a time, and it accepts the following annotation types: Entrez Gene ID, Genbank Accession, Refseq Accession, and Gene Name. If using Entrez Gene IDs, any "NA" values must be trimmed out of the gene list by going to the clipboard in the Gaggle Boss. Delete the "NA"s and the white space left behind, then click "Broadcast" and proceed as usual through Firegoose.
The Genome Browser
A very useful Goose is the ISB Genome Browser, a Java application that displays systems biology data on a genomic coordinate track. If MeV has chromosomal coordinate information loaded into its annotation model, it can broadcast expression data to the Genome Browser. There, the expression data will be displayed as a heatmap along with any other genomic tracks you chose to load. Full documentation for the Genome Browser is at that program's website.
To send expression data to the Genome Browser, right-click on one of MeV's many viewer windows, such as the KMC Experiment Viewer. Choose the popup menu option Broadcast matrix to Genome Browser. Since there is no Genome Browser currently running and connected to the Gaggle Boss, MeV will attempt to launch the Genome Browser via Java WebStart. MeV will also pop up a window explaining to you that you will need to load an appropriate genome into the Genome Browser. Follow the Getting Started instructions at the Genome Browser website to do this. When the genome is loaded, return to MEV's warning window and click OK.
If the Genome Browser receives the broadcast correctly, a window titled "Received Matrix Broadcast" will appear. You should be able to accept all of the defaults in this window. Your data should be in the browser now, though you may need to zoom out quite a bit to see it. Use the slide on the left-hand side of the window to do that.
Advanced Gaggle Use
Those who use the R or Matlab environments can make use of the available Goose plugins as well. A tutorial on these tools is beyond the scope of this document, and we refer you to the R Goose and the MatGoose websites.
Advanced MeV and Gaggle users may want to read the MeV and Gaggle developer documentation, which describes the various metadata values that can be included in both incoming and outgoing broadcasts to the Gaggle.