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| '''__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. | |
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1. Open website: 1. Logon with: un pw -> if problem switch to ppt 1. Click |
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| '''__Plugins to Load__''': Network and Attribute I/O, Network Inference, Functional Enrichment | ''__Cytoscape version__'': 2.4 - 2.6 |
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| '''__Data Files__''': Use the notch timeseries (Piet: refine this) |
''__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 1. Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon) 1. Click Timeseries: a panel provides you with three choices; 1. Select TableBuilder: 1. Choose cellline imr 1. Choose Notch1 1. tbc '''__Data Files__''': Notch timeseries (Piet: refine this) '''__Presentation__''': [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT] '''__Webstart__''': Time permitting '''__Video__''': Time permitting |
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:
Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi
Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon)
- Click Timeseries: a panel provides you with three choices;
Select TableBuilder:
- Choose cellline imr
- Choose Notch1
- tbc
Data Files: Notch timeseries (Piet: refine this)
Presentation: [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT]
Webstart: Time permitting
Video: Time permitting