[BioC] hyperGTest interpretation of 'under' and finding all Entrez associated with a GO term

[Steve Lianoglou]

Hi,

On Mon, Nov 12, 2012 at 9:30 AM, Mary Kindall <mary.kindall at gmail.com> wrote:
>    1.
>
>    How do I interpret the result of 'hyperGTest' if the argument
>    "testDirection='under'" is supplied? The hypergtest result is given below.

Are you looking for help in interpreting this test in a statistical
sense, or a biological one?

>    2.
>
>    Is there a way to find all Entrez IDs associated with a particular GO
>    term (For example, GO:0034660).

Here is the "old school" way -- I bet there is now a nicer way to do
this with the Homo.sapiens package (for instance). But let's say you
wanted all human genes that are annotated with SMAD binding
("GO:0046332")

R> library(org.Hs.eg.db)
R> head(org.Hs.egGO2ALLEGS[["GO:0046332"]])
R>   IDA   IDA   IDA   IDA   IDA   IDA
 "90"  "91"  "94" "650" "657" "658"

The names of the vector tell you the evidence code for the term ->
gene association

>    3.
>
>    How do I find list of all Entrez IDs which has a GO BP/CC/MF term? My
>    gene universe 'uGenes' initially had a total of ~22,000 genes, where as the
>    result below show it to be 19,703. This mean that some of my genes in the
>    universe did not have an associated GO term. How to find those which were
>    left out?

Once you have your GO term of interest, this is essentially the same
question (2), no?

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact