[BioC] Which resources for pathway analysis?

[January Weiner]

Dear Gilbert,

thanks for pointing me to GeneAnswers, this is definitely an
interesting tool. I have installed GeneAnswers using biocLIte.

However, in the documentation, I do find GO, DOLite and KEGG
mentioned, but not caBIO. How do I use GeneAnswers with caBIO?

Kind regards,

j.

> sessionInfo()
R version 2.10.1 (2009-12-14)
i486-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8       LC_NAME=C
 [9] LC_ADDRESS=C              LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] GeneAnswers_1.2.0   MASS_7.3-5          RSQLite_0.9-1
 [4] DBI_0.2-5           XML_3.1-0           annotate_1.24.1
 [7] AnnotationDbi_1.8.2 Biobase_2.6.1       RCurl_1.4-2
[10] bitops_1.0-4.1      igraph_0.5.5-1

loaded via a namespace (and not attached):
[1] tools_2.10.1 xtable_1.5-6


On Mon, Feb 28, 2011 at 4:49 PM, Gilbert Feng <g-feng at northwestern.edu> wrote:
> Hi, January
>
> GeneAnswers integrates GO, DO, KEGG, and caBIO(NCI, Reactome and Biocarta)
> as well as gene interaction and entrez keywords search for gene set
> enrichment analysis. Finally, it can automatically generate a html report
> for one or multiple groups of gene set enrichment analysis with interactive
> networks.
>
> Best
>
> Gilbert
>
>
>
> On 2/28/11 9:43 AM, January Weiner wrote:
>>
>> Dear all,
>>
>> my tool of choice currently is SPIA, a package that seems to provide
>> sophisticated analysis of pathways (including both, gene set
>> enrichment analysis and pathway perturbation analysis). I wonder what
>> other tools you could recommend? The task at hand is to identify
>> differentially regulated pathways given information on differentially
>> expressed genes, using a solid, but broad pathway database.
>>
>> There is, of course, a wide range of tools outside of R (e.g.
>> PathVisio) which can be used for data mining and visualisation as well
>> as running specific statistical analyses. I wonder what are you using
>> in R.
>>
>> kind regards,
>>
>> j.
>>
>
>



-- 
-------- Dr. January Weiner 3 --------------------------------------
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin, Germany
Web   : www.mpiib-berlin.mpg.de
Tel     : +49-30-28460514