Reactome Fi Plugin Cytoscape Help

Question

[Tanvi]

Reactome FI Plugin cytoscape help

I have microarray data and using reactome FI plugin in cytoscape I want to build gene interaction network.

After loading the expression data (1st column gene name and other columns samples with respective values) it is showing 0 modules in table as a result of MCL clustering with default parameters. And hence it is not giving the network output.

I dont know what is going wrong.

Thanks in advance !!

[Chris Evelo]

Which Cytoscape version are you using (should be 2.7.0 or above)

Answer 1

[Robin Haw]

The Reactome FI plugin does not include example files when you download the jar fle. However, if you go to the Reactome FI plugin User Guide (also accessible from the Cytoscape plugins menu>Reactome FIs>User Guide), you will find a number of example files that can be used with the Reactome plugin.

If you have any further questions please contact me at the Reactome helpdesk ([e-mail]).

Robin

Answer 2

[Tanvi]

Version is 2.8. I have downloaded a few weeks ago. There is no example file provided by reactome FI plugin tutorial. Hence I am not getting if I am missing something in the input gene expression file.

[Chris Evelo]

You could just have asked this information to your question (using edit). It is not an answer but more info about your question.

Answer 3

[Chris Evelo]

In that case I would e-mail the Reactome team and ask them to add an example data set to the tutorial. That will probably help more people and in my experience they are very helpful.