Cytoscape Wiki|
Size: 589
Comment:
|
Size: 2215
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 6: | Line 6: |
| '''__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. | |
| Line 9: | Line 10: |
| ''_Plugins to Load_'': Network and Attribute I/O, Network Inference, Functional Enrichment | ''__Cytoscape version__'': 2.4 - 2.6 |
| Line 11: | Line 12: |
| ''__Plugins to Load__'': R2Plugin, [http://chianti.ucsd.edu/cyto_web/plugins/index.php BiNGO], [http://baderlab.org/Software/NetMatch NetMatch] | |
| Line 12: | Line 14: |
|
1. Open website: 1. Logon with: un pw -> if problem switch to ppt 1. Click |
''__GUI steps__'': |
| Line 16: | Line 16: |
|
|| ''Story'' || ''Action'' || ''Remarks'' || || 1. Research into childhood tumors. Array data analyzed using web-based R2. Biologists use tumor series to extract relevant genes. These are manipulated in tumor cell-lines using siRna || Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi || || || 2. Access and datasets input still restricted; will change. For logon mail r2-support_at_amc.uva.nl || Logon with: un pw || If problem switch to ppt (Piet: todo provide restricted access logon) || || 3. R2 portal shows; menu reflects all possibilities, lots of data (>17,000 arrays), clinical data, all types of stat analysis || Click Timeseries || || || 4. Panel provides you with three choices: __Explore timeseries__: single gene in series; __TableBuilder__: Find genes in series based on tresholds; __Multiplo__: Limma statistics applied to replicates. Availability of other datasets under dropdown || Select TableBuilder || Keep default selection set_hg_mix, upcoming improved naming of these sets || || 5. || Choose cellline imr || || || 6. || Choose Notch1 || || || || || || || || || || || || || || |
|
| Line 17: | Line 27: |
| '''__Data Files__''': Use the notch timeseries (Piet: refine this) | '''__Data Files__''': Supplied via website R2 |
| Line 19: | Line 29: |
| '''__Presentation__''': TBD | '''__Presentation__''': [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT] |
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. Research into childhood tumors. Array data analyzed using web-based R2. Biologists use tumor series to extract relevant genes. These are manipulated in tumor cell-lines using siRna |
Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi |
|
2. Access and datasets input still restricted; will change. For logon mail r2-support_at_amc.uva.nl |
Logon with: un pw |
If problem switch to ppt (Piet: todo provide restricted access logon) |
3. R2 portal shows; menu reflects all possibilities, lots of data (>17,000 arrays), clinical data, all types of stat analysis |
Click Timeseries |
|
4. Panel provides you with three choices: Explore timeseries: single gene in series; TableBuilder: Find genes in series based on tresholds; Multiplo: Limma statistics applied to replicates. Availability of other datasets under dropdown |
Select TableBuilder |
Keep default selection set_hg_mix, upcoming improved naming of these sets |
5. |
Choose cellline imr |
|
6. |
Choose Notch1 |
|
|
|
|
|
|
|
|
|
|
Data Files: Supplied via website R2
Presentation: [attachment:PietMolenaar_ICSB_23_8_08.ppt R2AndCytoscape_PPT]
Webstart: Time permitting
Video: Time permitting