[BioC] PANTHER in R.... Gene lists in sigPathway?

[Ovokeraye Achinike-Oduaran]

Thanks a bunch, Felipe.

Regards,

Avoks

On Tue, May 22, 2012 at 6:45 PM, Felipe Riveroll Aguirre
<friveroll at gmail.com> wrote:
> May be you can get the limma logFC associated values, for associated
> GWAS genes, in the example from SPIA, I started only with entrezID's
> from KEGG link, and grab the logFC values from limma in sig_genes
> vector
>
> sig_genes <- subset(top, adj.P.Val<0.01)$logFC
> names(sig_genes) <- subset(top, adj.P.Val<0.01)$ENTREZ
>
> with this code
>
> genes.both <- sig_genes[which(names(sig_genes) %in% genes.via.sel)]
>
> Where  genes.via.sel, was a gene list set of entrezID's to get limma
> associated values.
>
> So you can do an approach like this to get associated logFC values
> from associated GWAS genes
>
> Also there is another server I known for gene lists
>
> http://www.bioprofiling.de/R_spider.html
>
> Here you get an analysis combining signaling and metabolic pathways
> from Reactome and KEGG databases.
>
> So, R only helps to get the required inputs, for external web appz, or
> you can download pantherdb database and write an script for automate
> the whole process, from R output
>
> Best,
>
> Felipe
>
> 2012/5/22 Ovokeraye Achinike-Oduaran <ovokeraye at gmail.com>:
>>
>> Hi Felipe,
>>
>> Thanks. The thing is that I have genes from both GWAS and DE analysis from Limma in one list. So they don't all have logFC values, hence my question about gene lists and not necessarily gene sets. I ran my list through the PANTHER web interface and got some results but I just wanted to know if it had an R implementation.
>>
>> DAVIDQuery() might work if it gives the same options as is web interface of choosing the PANTHER pathway option but I didn't find the instruction manual very straightforward.
>>
>> Thanks again.
>>
>> -Avoks
>>
>
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