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looking for an expression analysis tool

Stefan Goetz stefang at fis.upv.es
Tue Jun 13 09:57:39 PDT 2006


Hi Jane, 
have you had a look at Blast2GO (www.blast2go.de)?
B2G allows you to import your own GO annotation data and take it to
further GO enrichment analysis.
(Screenshot: http://www.blast2go.de/screenshots/fisher.html)
Cheers Stefan.


B2G annotation text-file import format (yourAnnotation.annot) example:

Seq1 GO:0001234
Seq1 GO:0001264,GO:0004567,...
Seq1 GO:0034567
Seq2 GO:0001234,...
Seq2 GO:0001244
Seq3 GO:0001234,GO:0004567,GO:0009123
....
..
.
(between SeqID and GO-Term-ID as to be a tabulator)

More Info:
Blast2GO (B2G) joins in one universal application similarity search
based GO annotation and functional analysis. B2G offers the possibility
of direct statistical analysis on gene function information and
visualization of relevant functional features on a highlighted GO direct
acyclic graph (DAG). Furthermore B2G includes various statistics charts
summarizing the results obtained at blasting, GO-mapping, annotation and
enrichment analysis (Fisher's Exact Test). All analysis process steps
are configurable and data import and export are supported at any stage.
The application also accepts pre-existing blast or annotation files and
takes them to subsequent steps. The tool offers a very suitable platform
for high throughput functional genomics research in non-model species.
B2G is a species-independent, intuitive and interactive desktop
application which allows monitoring and comprehending the whole
annotation and analysis process supported by additional features like GO
Slim integration, evidence code (EC) consideration, a Batch-Mode or
GO-Multilevel-Pies. 


 ------------------------------------------------------------
 | Stefan Götz - stefang(at)fis.upv.es                      |
 | IBM - Biomedical Informatics, Bioinformatics Area        |
 | BET - Bioengineering, Electronics and Telemedicine Group |
 | UPV - Politechnical University of Valencia - Spain       |
 ------------------------------------------------------------ 


> -----Original Message-----
> From: owner-gofriends at genome.stanford.edu 
> [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Jane Lomax
> Sent: Tuesday, June 13, 2006 4:24 PM
> To: gofriends at genome.stanford.edu
> Subject: looking for an expression analysis tool
> 
> 
> Hi - does anyone devevelop, or know of, a gene expression 
> analysis tool 
> that uses GO, and allows a user to upload their own gene 
> association file, 
> preferably in standard GO format?
> 
> This is useful for species with no GO annotation in the GO database.
> 
> many thanks,
> 
> Jane
> 
> -- 
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
> 
> p: +44 1223 492516
> f: +44 1223 494468
> 
> --
> This message is from the GOFriends moderated mailing list.  A 
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> 



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