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

Paola Roncaglia paola at ebi.ac.uk
Thu Jun 28 13:10:09 PDT 2012


For archive.
Paola

-------- Original Message --------
Subject: 	Re: [go-friends] GO enrichment analysis - IDs not in database
Date: 	Thu, 28 Jun 2012 13:00:45 -0700
From: 	Nathan Salomonis <nsalomonis at gladstone.ucsf.edu>
To: 	Paola Roncaglia <paola at ebi.ac.uk>



Great!
Nathan


On 6/28/12 12:52 PM, "Paola Roncaglia"<paola at ebi.ac.uk>  wrote:

>  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
>>



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