[BioC] package for pathway analysis

Marc Carlson mcarlson at fhcrc.org
Tue Aug 10 21:09:15 CEST 2010

Just to add one more little thing to Wolfgangs terrific post, the
GOstats package also has some nice vignettes that can get you started
using this stuff with GO which is a very common thing people want to do
when they are asking these kinds of questions.  And it is also possible
to do a similar thing using KEGG annotations which might be a good match
for your metabolic pathway questions.



On 08/10/2010 07:32 AM, Wolfgang Huber wrote:
> Dawn,
> have a look at the Category, GSEABase, topGO and BioNet packages and
> in particular their vignettes. Check also: Bioinformatics. 2008 Nov
> 15;24(22):2586-91. Gene set enrichment analysis using linear models
> and diagnostics. Oron AP, Jiang Z, Gentleman R.
> Apologies to everyone I did not mention - there is a lot of good
> literature (and software) on gene set enrichment analysis out there,
> which I will not try to review here, entering "gene set enrichment
> analysis" in Pubmed or Google Scholar would be a good start.
>     Best wishes
>     Wolfgang
> Dawn scripsit 08/08/10 12:50:
>> Hi,
>> I have two groups(one is for control) of genomic data and try to do
>> metabolic pathway analysis using Bioconductor. Would you please give
>> me some
>> suggestion about what packages I should use and the information about
>> how I
>> can start (e.g., the tutorial )? I hope to see which genes are up and
>> down
>> in particular pathwa*y such as the insulin pathway.*
>> *
>> *
>> *Thank you very much!*
>> *Dawn*
>>     [[alternative HTML version deleted]]
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