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

[Felipe Riveroll Aguirre]

There is no bioconductor project, for pantherdb, but you can get a tab
separated file with entrezID and logFC data from limma for example,
and upload the generated file to the pantherdb website and use Tools>GENE
EXPRESSION DATA ANALYSIS>Analyze a list of genes with expression
values to get a pathway analysis

May be this could help you, I had done somethin similar with SPIA to get a
KEGG heatmap from a selected pathway here:

http://translate.google.com/translate?sl=auto&tl=en&js=n&prev=_t&hl=en&ie=UTF-8&layout=2&eotf=1&u=http://blog.feliperiveroll.name/obtencion-de-un-heatmap-para-una-via-de-senalizacion/&act=url

The main idea was to parse the SPIA pathway output link, and get the
KEGG identifier for this pathway, the KEGG identifier of an object in
this pathway, and finally the logFC value, and feed a external python
script to get the heatmap.

You can read more about the SPIA (and pathway) analysis, here
http://gettinggeneticsdone.blogspot.mx/2012/03/pathway-analysis-for-high-throughput.html

And also, panther could help you for a gene analysis for entrezID's

Hope it helps

Felipe Antonio Riveroll Aguirre, QFB
Departamento de Bioquímica
Laboratorio 26
CINVESTAV, México D. F.
CP 07360
Tel. +52 (55) 5747-3800 ext 5217
Celular. +52 (55) 3351-2251
Sitio web: http://www.feliperiveroll.name




2012/5/21 Ovokeraye Achinike-Oduaran <ovokeraye at gmail.com>:
> Hi all,
>
> Is there any way to execute PANTHER in R? And is there any possible
> way sigPathway works with gene lists in place of expression data?
>
> Thanks.
>
> -Avoks
>
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