Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[gofriends] tool to visualise terms in GO tree

Stefan Goetz sgoetz at cipf.es
Fri May 25 07:24:21 PDT 2007


Hi Kangwen and Jane, 
GO visualization is one of Blast2GOs main features. Load you annotations
(file->import->annotation->file.annot) like:
gene1 <tab> GO:000123,GO:000124
gene2 <tab> GO:000567
...
and than generate a "Combined graph" applying filters and coloring
parameters. 
Tree visualization is not supported since we don't think that this is a
very intuitive way of exploring GO DAG hierarchy. 
Export the graph data and statistical graphs/pies can be generates as
well. 
For more information the tutorial on our website
(http://blast2go.bioinfo.cipf.es) may help - or write us a mail.
To run Blast2GO you just need Internet and Java.
Good luck!
Stefan

PD.: 
http://www.geneontology.org/GO.tools.other.shtml#blast2go
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. 


> -----Original Message-----
> From: owner-gofriends at genome.stanford.edu 
> [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Jane Lomax
> Sent: Friday, May 25, 2007 5:43 PM
> To: gofriends at genome.stanford.edu; GO Help List; dengk at wyeth.com
> Subject: [gofriends] tool to visualise terms in GO tree
> 
> 
> Hello - does anyone have a tool that would be able to help 
> this user please?
> 
> thanks,
> 
> Jane
> 
> 
> contactName: Kangwen Deng
> contactEmail: dengk at wyeth.com <mailto:dengk at wyeth.com>
> contactText: Suggestion needed!
> I applied sigPathway analysis to my microarray (rat affy 
> 230.2.0)results 
> and got a list of GO terms that are over-represented. What I 
> want to do 
> is: link all these GO terms to visulize them in a GO tree. DO 
> you know 
> which tool can do this? Thanks.
> 
> 
> --
> This message is from the GOFriends moderated mailing list.  A 
> list of public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: 
> owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   
> gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  
> gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/
> 


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list