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

Paola Roncaglia paola at ebi.ac.uk
Thu Jun 28 12:52:14 PDT 2012


Dear Nathan,

Many thanks for your suggestions. I am forwarding your email to our user 
who might contact you directly if needed.

With best regards,
Paola Roncaglia

On 6/28/12 5:29 PM, Nathan Salomonis wrote:
> I would also like to recommend our software GO-Elite:
> http://genmapp.org/go_elite
>
> GO-Elite is a flexible platform that can create databases easily for any
> species using its graphical user interface. All that is needed are a couple
> of tab-delimited text files. These will include a gene to GO or gene to
> pathway association file, gene annotation file (symbol and description) and
> optionally an indirect identifier to curated gene identifier (model organism
> database ID or MOD) table (e.g., Affymetrix ID to MGI).  Gene Ontology
> hierarchy relationships can be automatically imported and updated as well
> from any source you like. A tutorial for adding new species support is
> provided here:
> http://code.google.com/p/go-elite/wiki/Tutorial_Adding_New_Species
> Also see:
> http://genmapp.org/go_elite/help.htm#new_species
>
> If you want a quick way to identify putative enriched biological GO terms or
> biological pathways you can also provide orthologous gene symbols as your
> input and denominator identifiers (SystemCode: Sy), after downloading the
> appropriate orthologous species database.
>
> You can check out our paper at:
> http://bioinformatics.oxfordjournals.org/content/early/2012/06/27/bioinforma
> tics.bts366
>
> Let us know if you have any questions.
>
> Best,
> Nathan
>
>
> On 6/28/12 8:48 AM, "Paola Roncaglia"<paola at ebi.ac.uk>  wrote:
>
>> 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
>

-- 
Dr Paola Roncaglia
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD
p: +44 1223 492600
f: +44 1223 494468



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