[Gramene] GO analysis of RNA-Seq data

[Pankaj Jaiswal (OSU)]

Try the following  URL and click on the table icon for results on the 
left side column above 'DATASET'. The tool will allow you to filter 
genes by MSU6/7 IDs as well.

http://www.gramene.org/biomart/martview/51792fa1e58261d266d47129a5d67cde/51792fa1e58261d266d47129a5d67cde/51792fa1e58261d266d47129a5d67cde?VIRTUALSCHEMANAME=default&ATTRIBUTES=osativa_eg_gene.default.feature_page.ensembl_gene_id|osativa_eg_gene.default.feature_page.go_accession|osativa_eg_gene.default.feature_page.go_name_1006|osativa_eg_gene.default.feature_page.go_namespace_1003&FILTERS=&VISIBLEPANEL=resultspanelhttp://www.gramene.org/biomart/martview/51792fa1e58261d266d47129a5d67cde/51792fa1e58261d266d47129a5d67cde/51792fa1e58261d266d47129a5d67cde?VIRTUALSCHEMANAME=default&ATTRIBUTES=osativa_eg_gene.default.feature_page.ensembl_gene_id|osativa_eg_gene.default.feature_page.go_accession|osativa_eg_gene.default.feature_page.go_name_1006|osativa_eg_gene.default.feature_page.go_namespace_1003&FILTERS=&VISIBLEPANEL=resultspanel

-Pankaj

On 11/5/2012 9:45 AM, Pankaj Jaiswal (OSU) wrote:
> 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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>