ncRNA-DB
The non-coding RNA human interaction Data Base.

ncINetView is a GUI client Cytoscape App to retrieve data from the ncRNA-DB data base server instance.

See the instructions in section Installation about how to install and run ncINetView in Cytoscape.
Section Documentation shows some usage examples.

Download

Download the ncINetView App for Cytoscape 3.x.

NOTE: the ncINetView App DOES NOT work properly if Cytoscape is not run from command line and if the Cytoscape enviroment directives are not properly settled. See Running ncINetView in Cytoscape.

download ncINetView ncINetView Cytoscape App.
v1.0.2 October 2014

License

ncINetView is a Cytoscape 3 App client interface for the ncRNA-DB database, released under the terms of the LGPL.

Installation

The ncINetView App can be installed from the Cytoscape App Manager (Apps → App Manager). Once you have downloaded the ncINetView App package, open Apps → App Manager, click on the "Install from File..." buttom and select the ncINetView package file (ncINetView-1.0.2.jar). See section Installing Apps on the official Cytoscape User Manual. The ncINetView will appear in the Apps Cytoscape menu bar.

The ncINetView App will be soon available on the Cytoscape App Store.

Running ncINetView in Cytoscape

In order to allow the ncINetView App to work properly under Cytoscape 3.x, you need to setup the Cytoscape runtime environment and run Cytoscape from the command line.

To setup the Cytoscape runtime enviroment, edit the file Cytoscape.vmoptions located in your Cytoscape installation directory. Add the following directive to the initial line of the file (preceded by a space) : -Dorg.osgi.framework.bootdelegation=sun.misc

Cytoscape has two distinct running modalities, through the Cytoscape exacutable (namely the defult launch icon which refers to Cytoscape.exe for Windows users, Cutoscape.app for OSX user and Cytoscape for linux users), or by running it from the command line. You need to run Cytoscape from the command line in order to enable Cytoscape to follow the addictional runtime directives, through the script cytoscape.sh for Linux and OSX users or cytoscape.bat for Windows users.
See also section Run Cytoscape from Command Line on the official Cytoscape User Manual.

NOTE: the ncINetView App DOES NOT work properly if Cytoscape is not run from command line and if the Cytoscape environment is not properly set up. In the second cae, the user obtain an error on the Cytoscape console reporting a Java exception reporting: Caused by: java.lang.ClassNotFoundException: sun.misc.Unsafe not found.

Documentation

Setting up the Cytoscape network

Before run ncINEtView over a Cytoscape Newotk, you may need to add two columns to the node table. A first column is needed to specify the biological entity type (NCRNA, RNA, GENE, DISEASE, OTHER) and it must by a Single column of type String. A second column is needed to input entity aliases using the ncRNA-DB RID format , and it must be a List column of type Aliases. You should specify such columns as Type column and Alias column, respectively, where required from the interface of ncINetView.

Add edges

Add nodes

Examples

Expanding the E2F6's network

This is an example of how to expand a gene network, adding linked ncRNA and gene-ncRNA interactions.

At first, we have created a new network with four genes (E2F6, EZH1, EZH2 and ARAF) and extracted their connections from the Biogrid data base.
Before running ncINetView we have created two additional columns in the cytoscape node table. One is a single value column of type String, and the other is an array column still fo tyep String. The first column serves to indicate the biological entity type, in this case it is GENE for all the four nodes. The second column server to indicate the aliases (by a list of ncRNA-DB RIDs) of such genes.

The pre-built network is available here.

Once the base network is ready, we can run ncINetView to extend it by searching for ncRNAs linked to the input genes and adding their connections. The image shows how to run ncINetView on the example network. The user needs to specify the input network to be extended, the column where biological types are specified and the column where entity aliases (ncRNA-DB RIDs) are indicated. Moreover, since the goal is to add ncRNAs linked to the input entitied and their interactions, the user needs to flag the "include neighbors" checkbox e select the ncRNA type.

The image below shows the final result after appling an "organinc layout" to the network view.
If input types and aliases had been specified well, and if there is a match with their RIDs inside the ncRNA-DB database, then a column named ncrnadb-rids will appear on the cytoscape node table. The column shows the ORIDs of matched entities. Moreover, further columns are created on the cytoscape edge table to show ncRNA-DB information for retrieved interactions.


Examples

Extracting the Hotair sub-network and extending it

This examples shows how to extracted the Hotair sub-network, namely how to search for biological entities linked to Hotair. After, the network is extended with extra disease entities, that are not connected to Hotair but are linked to its ncRNAs neighbors, and the interactions among such extra entities are retrieved.

Once a new Cytoscape network have been setted up (see above), Hotair and its neighborhood can be extracted by the Add nodes utility. After searching for Hotair (and getting a match on the ncRNA-DB database), you can extract its neighborhood by activating the include neighbours checkbox and all the biological entity types.

The figure shows the result of the neighborhood import, after a Group Attribute Layout on the column type is applied.

Now, we want to extend the previous netowrk with additional disease entities that are connected only with ncRNAs entities. The Add edges utility allows to do that by specifying just the ncRNA type for the alias column and incliding only the neighbors of type Disease. The utility just searches for new diseases (not yet in the network) that are connected to a ncRNA (already in the network).

The result of the last step is shown in the figure below.

The previous step only added interactions between ncRNAs and new retrieved Diseases. If you want to obtain the entire interaction set among all the entities now included in the netowrk, then you can re-apply the Add edges utility.

ncRNA-DB - The non-coding RNA human interaction database.