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    

[go-friends] GO enrichment analysis - IDs not in database

Calin Voichita calin at wayne.edu
Thu Jun 28 09:18:12 PDT 2012


Hello,

Our tools (Onto-Express / OE2GO) available at
http://vortex.cs.wayne.edu/ontoexpress/ are able to deal with such
situations. After logging in, please select OE2GO and an input form will
appear that requires:

- differentially expressed transcripts (which is available)
- the list of all transcripts (which should be available as well)
- the annotation (which I see its available)
- the ontology (in obo format that can be downloaded at
http://www.geneontology.org/GO.downloads.ontology.shtml) - currently we
only support v1.0

Don't hesitate to contact us for any further details.

Sincerely,
Calin Voichita

-------- Original Message  --------
Subject: [go-friends] GO enrichment analysis - IDs not in database
From: Paola Roncaglia <paola at ebi.ac.uk>
To: go-friends at lists.stanford.edu
Cc: go-helpdesk at mailman.stanford.edu, "a.weig at
uni-bayreuth.de"@domain.invalid
Date: Thu 28 Jun 2012 11:48:06 AM EDT

> Hello,
> 
> We have a GO user (cc'd on this email) who would like to perform GO term
> enrichment analysis on a newly sequenced species, from in-house
> microarray results. The genomic data is public (released by DOE-JGI),
> but not available from a public database yet, therefore the gene product
> IDs are not recognized by e.g. AmiGO's enrichment tool. The user has a
> list of IDs of differentially expressed transcript, and a table provided
> by the sequencing lab that contains all transcript IDs and
> automatically-generated GO term assignments. Could anyone please
> recommend a tool?
> 
> The latest email on this subject (containing most of the pertaining
> GO-help correspondence, bottom to top) is here:
> https://mailman.stanford.edu/pipermail/go-helpdesk/2012-June/005212.html
> 
> Many thanks,
> Paola Roncaglia
> 

-- 
Calin Voichita
Ph.D. Candidate
Intelligent Systems and Bioinformatics Laboratory (ISBL)
Department of Computer Science  - Wayne State University
Phone: +1(313)577-5070              Fax: +1(313)577-6868
Detroit, MI 48202, USA
http://vortex.cs.wayne.edu




More information about the go-friends mailing list