1. Visually Comparing Hi-C Networks: Demo Presentation CytoHiC in 10 Steps http://www.cl.cam.ac.uk/~ys388/CytoHiC

2. 1. Download CytoHiC Plugin*: http://www.cl.cam.ac.uk/~ys388/Cy toHiC/CytoHiCPlugin.jar http://www.cl.cam.ac.uk/~ys388/Cy toHiC/CytoHiCPlugin.jar * Make sure you have Cytoscape 2.8.3 (or later version) installed on your computer

3. 2. Place it in Cytoscape’s plugins directory

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

5. 4. Open the View Dialog

6. 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/ 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

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

8. 6. Click OK: a network will be generated

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

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

11. 9. Compare Hi-C networks a. Use indices to compare landmarks b. Use hovering and browsers to view landmarks details

12. 10. Learn more with CytoHiC’s user guide