What Does “Du” Mean In Sif File And How I Can Visualize This File ?

Question

[someone]

Hello,

I work in SynTReN program

http://www.biomedcentral.com/1471-2105/7/43/

That creates Gene Network

I have two questions please:

1-The result of this program is file that contains like that:

envY_ompT ac ompF    
lrp ac ompF    
lrp re lrp    
bgr_nlpD_rpoS du bgr_katG
bgr_nlpD_rpoS du bgr_adhE

If “ac” means activation and “re” means repression, what does “du” mean?

2-Is there program that can visualize this network like that:

http://www.biomedcentral.com/1471-2105/7/43/figure/F5

The extension of the file is .sif

Thanks

Answer 1

[Neilfws]

To answer the second question: yes, there are lots of ways to visualize the network starting from the SIF file. One of them is Cytoscape; in fact, the SIF format is described at the Cytoscape wiki. It should also be easy to convert SIF into something recognised by Gephi. One more option: since the file is delimited text, it can be read into R for use with igraph.

So far I'm unable to find the meaning of "du", or even whether SIF relationship types (or edge types) are standard and defined somewhere. You may need to contact the authors for that.

[someone]

Thank you . your answer is very helpful for me.