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[go-friends] GO subgraph visualization

Stefan Götz sgoetz at cipf.es
Fri Feb 3 09:45:16 PST 2012


Dear Monica,
with Blast2GO you can visualize a list of GO terms (annotations)
as GO-Graphs.
Simply create a plain text file (with the extension: .annot) with two
columns like this:

GO:0001234<tab>GO:0001234
GO:0001235<tab>GO:0001235
GO:0001236<tab>GO:0001236
GO:0001237<tab>GO:0001237

or:
Condition1<tab>GO:0001234
Condition1<tab>GO:0001235
Condition2<tab>GO:0001236
Condition2<tab>GO:0001237

or:
gene1<tab>GO:0001234
gene2<tab>GO:0001235
gene3<tab>GO:0001236
gene2<tab>GO:0001237

(replace <tab> by a tabulator, you can do this e.g. with excel)

Save the file e.g. as: my_go_list*.annot* and open it with
Blast2GO*(Menu->File->Load Annotations).
*
To run Blast2GO you need JAVA.
You can than visualize the functional information via GO-Graphs.
*(Menu-> Analysis->Make
Combined Graph)*
This graphs, containing your list of GO terms, can than be
filtered, colourized (e.g. by gene abundance), represented as pie-chart (GO
level and multilevel) and exported (as png, pdf, svg and txt).
Additionally, you may also apply a GO-Slim reduction to your list of GO
terms.

Best regards,
Stefan


On Fri, Feb 3, 2012 at 5:27 PM, Monica Chagoyen <monica.chagoyen at csic.es>wrote:

> Hi,
>
> Does anybody know a visualization tool to represent a GO subgraph
> containing a user-defined GO list of terms?
>
> Thanks in advance,
>
> Mónica
> --
> Monica Chagoyen
> Computational Systems Biology Group
> Centro Nacional de Biotecnologia - CSIC
> C/ Darwin 3, 28049 Madrid, Spain
> Email: monica.chagoyen at csic.es
> Phone: +34 915854676
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>
>
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