[BioC] Looking for a function
Steve Lianoglou
lianoglou.steve at gene.com
Wed Apr 16 23:24:26 CEST 2014
Hi Jerry,
On Wed, Apr 16, 2014 at 2:07 PM, Jerry Cholo <jerrycholo at gmail.com> wrote:
> Hello,
>
>
>
> In Bioconductor, I am looking for a function, in that the input of the
> function would be a word such as "inflammation", "fibrosis", or
> "apoptosis", and the output of the function should be the list of
> significant "gene symbols" associated with the input words. The degree of
> association will be evaluated by FDR or p-value. Basically, the function
> will use publicly available datasets. I appreciate if someone provide me
> the name of this function.
Dollars to donuts: there is no such function.
You could, however, ask what genes are annotated with a certain
function (ie. GO term).
For instance, query AmiGO to see what GO terms are associated with inflammation:
http://amigo.geneontology.org/amigo/search/ontology?q=inflammation
One such term is "GO:0002544" (chronic inflammatory response).
Given the GO:XXXX id, you can ask what genes are associated with it.
To start figuring out how to do that, this tutorial will likely help:
http://bioconductor.org/help/workflows/annotation/annotation/
And so, too, would googling for something like "bioconductor query go term"
HTH,
-steve
--
Steve Lianoglou
Computational Biologist
Genentech
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