Steps to get overrepresented regulatory motifs using the Cytoscape plugin 'Pathicular'.

This tutorial will guide through finding TRI-TRI path in deletion data for a 
cell cycle related transcription factor 'SWI4'.

1. Load the input networks: 
Networks of interest can be loaded in Cytoscape in different ways.
We will load it from a text file in this example. 

> Load two text files 'deletion_data' and 'chip_data' one after the other in Cytoscape using: File > Import > Network from Table.
> In the GUI for 'Import Network from Table', after selecting the appropriate file, select 1st column as 'source interaction' and 2nd column as 'target interaction'.

2. Running Pathicular: 
> In the 'Pathicular' tab, select 'deletion_data' in the first box.
> Select 'SWI4' from the list of transcription factors to find the path. 
> Select chip_data as a network in the first as well as the second box. Make sure that the 'directed' box is checked.
> Click on 'Execute'.

After running the program, a new network 'Pathways' will be created with all 'TRI-TRI' paths for the SWI4 transcription factor. This path is overrepresented with the P-value displayed on the 'Pathicular' tab.

3. Find individual regulatory paths:
> Click on 'Modularize' to get regulatory paths using different intermediate 
transcription factors ( 6 transcription factors - FZF1, HMS2, YAP5, NDD1, STP4
and TYE7 in this case).

The output of these steps is also included with this sample data as a .cys file (sample_cysfile.cys).


Hope you enjoyed it!!!

