Workflow 2

Workflow 1: Analyzing the statistical results of AltAnalyze
Workflow 2: Analyzing a protein interaction network
Workflow 3: Analyzing a gene interaction network

Installing DomainGraph

Download and install Cytoscape 2.6
Go to the plugins manager in the Cytoscape menu, 'Network inference' and select DomainGraph for install.
Start DomainGraph via the plugins menu.
Upon first usage you need to register and accept the DomainGraph license.

Installing the DomainGraph database (WITH internet connection)

Go to the plugins menu, select DomainGraph -> Manage DomainGraph database -> Import data for selected species into database.
Choose a local folder to install the database. Make sure to have write permission for this folder.
Select 'Homo sapiens'.
Select database version ENS_52.
Click on the import button.
Wait until a window pops up telling you the database is complete.

Installing the DomainGraph database (on a machine WITHOUT internet connection)

You first have to install the database on a computer that is connected to the internet, as described above.
Once you have installed the database, you can copy it to any other machine as follows:
Copy the database directory (the folder that you chose for the database) to the non-connected machine.
Example: You installed the database to "C:\Cytoscape\Database\" on the internet computer.
You copy the "Database" folder anywhere to the non-internet computer.
Go to the plugins menu, select DomainGraph -> Manage DomainGraph database -> Change path to database.
Choose the "Database" directory as new path.
The database can now be used on your non-internet computer.

Importing a protein interaction network into DomainGraph

This step requires a protein interaction network, given with Ensembl or UniProt ids. You can download a toy protein interaction network containing human proteins via right-click here. Save the file to your disk.

Go to the plugins menu, select DomainGraph -> Start DomainGraph.
Select 'Create domain graph for gene or protein interaction network'.
Click the Start button.
Select 'Visualize protein interaction network'.
Click on the drop-down menu to select/import protein interactions.
Select 'Import own network'.
Choose the location of your protein interaction network.
Click on the second drop-down menu to select domain interactions. Choose 'InterDom' as domain interaction dataset.
Leave the network view on 'extended' and identifier on 'UniProt'.
Click the Submit button.
The resulting domain graph consists of the input proteins and protein interactions and is enriched by the domain compositions and domain interactions occurring according to InterDom.
Your resulting network should look similar to this screenshot.

Integrating Affymetrix Exon Array data for Single Experiments

This step requires two preprocessed files, an expression data file and a p-value file, created with APT or Expression Console (see Preparing Affymetrix Exon Array data for further information). You can download a sample expression data file via right-click here. You can download the corresponding p-value file via right-click here. These sample files describe the expression in testis tissue. Save the files to your disk.

Go to the plugins menu, select DomainGraph -> Integrate Affymetrix exon expression data.
Select the 'Single Experiment' tab.
Click the Import button right of 'choose expression file'.
Select the expression sample data for import.
Type in a name for this dataset and click on Import.
Once the data is imported, it is shown in the drop-down menu.
Click the Import button right of 'choose p-value file'.
Select the p-value sample data for import.
Type in a name for this dataset and click on Import.
Once the data is imported, it is shown in the drop-down menu.
Click the OK button and wait for the data integration.
In the resulting domain graph, domains partly or completely not expressed (=spliced out) are highlighted in pink. Orange domains are those being normally expressed but would form interactions with a spliced-out domain.
Your resulting network should look similar to this screenshot.
In the results panel on the right you can see the proteins, domains, and probesets that are not expressed in the sample according to their DABG p-values.
Click on a row in the results panel to select the respective node in the network.

Viewing proteins, domains, exons, probesets, and miRNA binding sites as graphics

Double-click on the protein node labelled 'NTNG2' (you might have to zoom in to be able to read the node labels).
The graphics is displayed in the data panel and should look similar to this screenshot.
The top row of an entry shows the protein with its contained domains (colored rectangles).
Below is the exon structure including 5' and 3' UTRs.
Below are the probesets. Pink coloring indicates that the probeset is not expressed. A color gradient from yellow to red is applied for expressed probesets representing the expression strength.
Please note the absent probesets (colored in pink) covering most of the sequence of the Laminin-N domain and the 3rd Laminin-EGF domain.
The blue rectangle below one probeset indicates a microRNA binding site.
Move the mouse over the domains, exons, probesets, and miRNAs. Tooltips providing additional information are shown.
Move the mouse over the pink probesets. The tooltips display the p-values computed by DABG.
Right-click somewhere in the data panel. A menu will pop up for customizing and saving the graphics.
Click on an exon. This will open the corresponding Ensembl website for further information.