STRING/CYTOSCAPE/BiNGO

[gsp...@pasteur.fr]

Hello,

We are using STRING to search for networks and GO terms in our proteomics data sets generated for the protozoan parasite Leishmania. We visualized the results in Revigo but wanted to use Cytoscape for network and GO visualization. Below are my questions. Thank you very much in advance for your help. Gerald

1) I ran STRING using the Cytoscape plug in and its working very well. While I can nicely organize/format the interaction network/pathways, I was unable to benefit from the GO data that are generated in STRING – it seems that this information is lost when using the Cytoscape plug in. I would like  to ask your advice on how I can transfer the STRING GO data into Cytoscape and eventally the BiNGO plug in. For BiNGO I need to select an organism/annotation database but there is only Trypanosome brucei available. Could the Leishmania information be added here? Is this really required if we come from a Leishmania-specific STRING analysis? 

2) I can add the GO terms and statistics from STRING into Revigo and get various GO representations. There is a file that can be downloaded from Revigo to be used in Cityscape (file is *.XGMML.txt). However if I try to load it I am asked to define columns. Do I have to do a conversion from  XGMML.txt into XGMML? Or is there any other option to load this data?

[Scooter Morris]

Greetings,
   BiNGO can use any ontology (see the "Custom..." organism).  I'll also note that the STRING app will include enrichment analysis in the near future.

-- scooter