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

Nathan Salomonis nsalomonis at gladstone.ucsf.edu
Thu Jun 28 09:29:41 PDT 2012


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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