R2 and Cytoscape: Inferring gene targets by graph based integration and analysis of molecular biological data

Piet Molenaar

Academic Medical Center, University of Amsterdam, the Netherlands

Biological Use Case: In our lab we're doing research into the molecular networks involved in childhood cancer. To this end we've profiled a large set of childhood tumors. Guided by biological questions we set out to develop a web-based array analysis platform called R2. In order to make an educated guess what genes to test that appeared of importance in this analysis we needed additional network analysis.

Recipe

Cytoscape version: 2.4 - 2.6

Plugins to Load: R2Plugin, BiNGO (Piet: provide link), NetMatch (http://baderlab.org/Software/NetMatch)

GUI steps:

1. Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi

2. Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon)

3. Click Timeseries: a panel provides you with three choices;

4. Select TableBuilder:

5. Choose cellline imr
6. Choose Notch1
7. tbc

Data Files: Notch timeseries (Piet: refine this)

Presentation: [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT]

Webstart: Time permitting

Video: Time permitting