Download GRN plugin The GRN query plugin expects to receive input data in

USER MANUAL
GRN plugin
The GRN query plugin is designed to retrieve the transcriptional regulatory information
within undirected coexpression network. It utilizes regulatory knowledge from the databases
Transcriptional Regulatory Element Database (TRED)(Jiang, Xuan, Zhao, & Zhang, 2007),
Molecular Signatures Database (MSigDB) (Liberzon et al., 2011) and JASPAR database
(Sandelin, Alkema, Engström, Wasserman, & Lenhard, 2004).
Invoking the GRN Plugin
The GRN query plugin can be initiated from the menu bar Window > GRN
Input data
The GRN query plugin expects to receive input data in tabular form, with each line in
the file representing a regulation link (from_node, direction, to_node).
For example, a sample file with 14 regulation links and 11 genes with this format
might look as follows:
Sp2
Sp2
Sp2
Sp2
Sp2
Sp2
Sp2
Sp2
Sp2
Wt1
Wt1
Wt1
Wt1
Wt1
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
undirected
Th
Tnfrsf23
Tsix
Usp29
Wt1
Xlr4c
Zim1
Zim2
Zim3
Xlr4c
Zfp264
Zim1
Zim2
Zim3
The user can load the input co-expression network using the button “choose network file”
Then, the plugin will calculate automatically the number of edges and nodes in the loaded
network
Plugin options
The options panel can be invoked from preferences > plugins > GRN plugin tab.
The application gives the user the options to select the databases of interest to retrieve the
regulatory information from and also identify some parameters related to each one such as the
species, and automatic update with every run.
Additionally, the user can set the binding motif parameters such as the length of considered
promotor region, and whether taking the motif complement into consideration or not.
Moreover, the user has the option to expand the network by (a) adding further transcription
factors that are annotated as known regulators of the input gene network, and /or by (b)
including additional target genes that are annotated to be regulated by the TFs in the input
network, and /or (c) searching for regulation interactions between the additional target genes
and the additional TFs
Create a task
After setting all parameters, user needs to create a task by pressing the button “create task” to
register this plugin run into the task queue.
Finally, to run the plugin, click menu bar “Task” > “Run Tasks”
Output
After finishing the task, the resulting GRN network will be displayed in the network panel
(network tab). This graphical display is user interactive and indicates whether the edge is
directed or not. The application uses force directed algorithms to layout the nodes and make
the network aesthetically displayed as much as possible. Nevertheless, the layout is
sometimes heuristic and is not always good. Therefore, we advice the user to use the mouse to
move the nodes and edges around to manually create a more readable layout.
The output GRN network displayed in the network panel. Transcription factors involved in the
input network are identified and marked in yellow, while the remaining genes are in blue.
Marked in orange the additional transcription factors; while the additional target genes are
marked in green. The edge labels depicts the confidence level of the corresponding regulation
link.
Also, one can export the network as an image or as a network file (.sif) to be imported, and
visualized by other network analysis tools like Cytoscape (Smoot, Ono, Ruscheinski, Wang,
& Ideker, 2011) or Visant (Hu et al., 2013).