[Gramene] GO analysis of RNA-Seq data

[Pankaj Jaiswal (OSU)]

Hi Ann,

The beset way to get all the GO annotation sis by using the BioMart\
http://www.gramene.org/biomart/martview

Select 'plant genes' followed by 'oryza sativa genes MSU6' and follow 
the attributes section to get GO. Together with Plant-Ensembl, we run 
our own pipeline to get the detailed GO annotations on genes that is not 
limited to GO-slim.

Let me know if it helps.

Best
Pankaj


On 10/29/2012 10:50 AM, Loraine, Ann wrote:
> Sorry to bother you!
>
> I didn't realize that MSU has already annotated the genes in MSU7 using
> GOSlim terms, which I think will meet my needs:
>
> ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.GOSlim_assignment
>
> I got the file from them and am using it that one for now.
>
> Thank you and I hope all is well despite the hurricane.
>
> Best,
>
> Ann
>
> -------------------------------
> Ann Loraine, Ph.D.
> Associate Professor
> Department of Bioinformatics and Genomics
> University of North Carolina at Charlotte
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> aloraine at uncc.edu
> http://www.transvar.org
> http://www.bioviz.org
> http://www.uncc.edu
>
>
> From: Ann Loraine <aloraine at uncc.edu <mailto:aloraine at uncc.edu>>
> Date: Sun, 28 Oct 2012 18:42:56 -0400
> To: <gramene at gramene.org <mailto:gramene at gramene.org>>
> Subject: GO analysis of RNA-Seq data
>
> Hello,
>
> I am using GOSeq (Bioconductor package) to analyze some RNA-Seq data
> from rice.
>
> I'm writing to ask your advice on how to best use the rice GO
> annotations Gramene has provided on the geneontology.org Web site.
>
> I have differential expression information for genes annotated as part
> of the (latest) MSU7 gene annotations release.
>
> (I made it by aligning my reads against the assembly. I then counted
> reads that overlapped the MSU7-annotated gene models.)
>
> However, it is not entirely clear how to map rice genome locus ids (such
> as LOC_Os06g31210) onto the Gene Ontology category annotations listed in
> the gene association file (gene_association.gramene_oryza.gz) available
> from geneontology.org.
>
> I see that some of the lines contain ids such as LOC_Os06g31210, which
> look like gene ids from the MSU annotations.
>
> My question is: can you explain how I should map MSU7 locus ids onto the
> GO ids listed in the file?
>
> It looks like you were using the Uniprot id as the primary key. If I
> could get a mapping between Uniprot id and MSU7 locus identifiers, that
> would probably be enough.
>
> Could you let me know what the best way to do this would be?
>
> I can easily run blast, blat, or write a simple program to match fields
> across files. For example, I could extract the genomic sequence for each
> gene model and then use blastx to identify the best hit protein id from
> SwissProt/UniProt. If the GO file is using the Uniprot id as the primary
> key, then I could link locus ids to GO terms using the best hit from
> Uniprot.
>
> Does this sound like it would work or would you recommend a more
> straightforward path?
>
> Thank you so much for the Gramene resource and for providing the GO
> annotations!
>
> Best wishes,
>
> Ann Loraine
>
> -------------------------------
> Ann Loraine, Ph.D.
> Associate Professor
> Department of Bioinformatics and Genomics
> University of North Carolina at Charlotte
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> aloraine at uncc.edu <mailto:aloraine at uncc.edu>
> http://www.transvar.org
> http://www.bioviz.org
> http://www.uncc.edu
>
>
>
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