[Gofriends] questions on GO grid visualization

[Stefan Goetz]

Dear Lei,
the GO-Graph-Viewer at www.babelomics.org should do the work.
There is also a free desktop application to analyze GO-data called 
Blast2GO. It makes combined graphs of annotated GeneSets among many 
other things.
If you want to colorize nodes in a GO- Graph (btw. its rather DAG than a 
GridGraph) depending on the degree of enrichment in both cases 
(go-graph-viz and blast2go) you would have to format your data like 
given below rather than as a matrix:
geneName<tab>goId<tab>pvalue
If you need any further help with this please let me know or have a look 
at:
http://bioinfo.cipf.es/babelomicswiki/tool:gographviz
or http://www.blast2go.org 
Best regards,
Stefan Goetz

PD.:
High-throughput functional annotation and data mining with the Blast2GO 
suite - NAR(2008)
http://nar.oxfordjournals.org/cgi/content/abstract/gkn176v1

--------------------------------------------
Stefan Götz
Bioinformatics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------


DU Lei wrote:
> Hi, all,
>
> I was hoping someone could help me with these two questions:
>
> 1. for a gene-GOterm adjacent matrix, is there any tool for drawing a
> grid graph of this?
>
> 2. for a GeneSets-GOterm matrix, with each number shows the enrichment
> degree of the corresponding gene sets and the GOterm(eg. the p-value I
> got from GOstat(gostat.wehi.edu.au)), i drew a heatmap for this
> GeneSets-GOterm matrix to illustrate the GOterm existence across
> GeneSets. Intrinsically GOterms have internal structures, how could I
> adjust this heatmap to show both GOterm existence as well as their
> structures? Or is there any tool to draw a heatmap for this case?
>
> Thank you!
> _______________________________________________
> Gofriends mailing list
> Gofriends at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/gofriends
>


-- 

--------------------------------------------
Stefan Götz
Bioinformatics Department
Centro de Investigación Príncipe Felipe (CIPF)
C/E.P. Avda. Autopista del Saler, 16-3 (junto Oceanográfico)
46013 Valencia, Spain
Tel: +34 963289680 Ext. 1011
Fax: +34 963289574
E-Mail: sgoetz at cipf.es
http://bioinfo.cipf.es
--------------------------------------------