Transcription Network With Edges Type

Question

[Asaf]

Hi,

I was wondering where can I find transcriptional regulatory networks, of any organism, that include the type of edge i.e. activation or repression. There is such a network for E. coli in RegulonDB but all the other networks I found (e.g. for Yeast) included interactions between TF and genes but lacked the type of interaction. Does anybody know such a network? Thanks

Answer 1

[Khader Shameer]

I would start first with FANTOM 4, also see this manuscript. FlyBase have extensive genetic interaction data (enhancers or suppressors), am sure other model organism database will have similar datasets. Another option is to scan STRING for PPI interactions mediated by TFs.You can filter the interactions based on "actions" (Activation, Inhibition, Binding... ); example here.

[Asaf]

Thanks! However, I couldn't find a way to download the data from FANTOM4 nor from flybase. I got the interactions from STRING but the networks there are partial, E. coli for instance has only 192 edges whereas the RegulonDB has thousands and this network is one of the biggest STRING have.