Visually Comparing Hi-C Networks: Demo Presentation

CytoHiC in 10 Steps

http://www.cl.cam.ac.uk/~ys388/CytoHiC

1 .Download CytoHiC Plugin :*:// . . . . /~ 388/http www cl cam ac uk ys CytoHi

/ .C CytoHiCPlugin jar

* Make sure you have Cytoscape 2.8.3 (or later version) installed on your computer

2 .Place it in Cytoscape’s plugins directory

3 .Launch Cytoscape: CytoHiC menu will appear under the Plugins

menu

4 .Open the View Dialog

5. Upload a bin file, a contact file and a landmarks file*

Example files are available at: http://www.cl.cam.ac.uk/~ys388/CytoHiC/Examples/

The genomic location of each segment (bin)Contact values between bins

The genomic location of landmarks of interest

*Example Files http://www.cl.cam.ac.uk/~ys388/CytoHiC/Examples/

6 .Click OK: a network will be generated

7 .Explore the network by hovering or through the node/edge browser

8 .Use the right click menu or the CytoHiC menu to compare networks

9 .Compare Hi-C networks

a. Use indices to compare landmarksb. Use hovering and browsers to view landmarks details

10 .Learn more with CytoHiC’s user guide