[BioC] Looking for a function

[Steve Lianoglou]

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