Cytoscape Wiki
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, [http://chianti.ucsd.edu/cyto_web/plugins/index.php BiNGO], [http://baderlab.org/Software/NetMatch NetMatch]
GUI steps:
Story |
Action |
Remarks |
1. Using tumor series to extract relevant genes |
Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi |
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2. Access and datasets input still restricted; will change. For logon mail |
Logon with: un pw |
if problem switch to ppt (Piet: todo provide restricted access logon) |
3. |
Click Timeseries |
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4. Panel provides you with three choices: _Explore timeseries_: single gene in series; _TableBuilder_ availability of other datasets and upcoming improved naming of these sets |
Select TableBuilder |
Keep default selection set_hg_mix |
5. |
Choose cellline imr |
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6. |
Choose Notch1 |
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Data Files: Notch timeseries (Piet: refine this)
Presentation: [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT]
Webstart: Time permitting
Video: Time permitting