[Gofriends] GO term enrichment analysis

[K. Shameer]

Dear Go Friends,

I am a member of this list for last six months. This is my first post to
the list.

I am working with experimental group in the computational annotation of
genes from  a high throughput RNAi experiment. We have screened 5000 genes
and we have got almost 500 genes as hits. Now we need to know the  GO term
enrichment of this set of 500 genes. I could see various programs
(standalone, webserver) are available that are available to perform GO
Term enrichment analysis .

I would like to know while performing such an analysis what are all the
statistical parameters I should take care of (Some tools have statistics
based on FDR, other are mostly P-Value based). Is there any reliable
command line program that can also be integrated to the database we are
developing ? Which program(s) are generally used by GO Friends for such
large scale analysis ?

Thanks in advance,
K. Shameer
NCBS - TIFR