stringApp functional enrichment

[Marwan Haioun]

Hello,

I have two questions relative to stringApp's functional enrichment in Cytoscape:

1. STRING provides more terms than Cytoscape does (16000 terms vs 4500 for my current network), can I change some parameters in Cytoscape to bring those numbers up?

2. I have noticed that we could do functional enrichment on clusters specifically, how can I download an enrichment table with cluster specific information? Right now it seems I can only download the enrichment for either all proteins or only one cluster at a time...

Thanks!

[Scooter Morris]

Hi Marwan,

I'll give a try at answering your questions:

1.  stringApp uses the same enrichment service that STRING does.  We do, however, set the FDR cutoff by default to .05.  At this point, there's no way to increase that.

2. Good suggestion.  I don't think you can at this point, but you are right that it would be a useful feature.  We'll add it to the list.

-- scooter

[Nadezhda Doncheva]

Hi Marwan,

Regarding the export of tables, it is indeed already on the list of features, we just have not gotten to it yet! Thanks for adding one more vote for this functionality :)

For the enrichment, I assume you perform it on the same set of nodes on STRING and in Cytoscape. In that case, you could also check the Filter icon in the STRING Enrichment table in Cytoscape and see if any of the filters are on. One possibility is that the redundancy filtering is on and that this leads to a different set of terms compared to STRING. Another option is to filter by different categories. 

If none of the filters is enabled, it might actually be a bug, so I would ask you to please share your session with me if you don't mind.

Best wishes, 

Nadya

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