Dear colleagues,

 I used to download GO database from geneoncology.org and did some c++ coding to manipulate the data as I wished. Now I want to try my luck with R - Bioconductor. I have heard of tons of tools supporting GO such as GO.db, topGO, goseq, GOstats, biomart etc... and I have been reading their description and examples, but honestly I am overhelmed and dont really know which package I should use to fulfill my task. So please advise me how I can do the following two simple tasks:

 1. I have a list of genes (with gene names from UCSC such as Foxp3 etc...). How do I filter this list to get genes that have certain GO term such as transcription factor?

 2. How do I know the capacity of the latest GO database on bioconductor, for example, how many genes available for mm9, and how many of them have GO term transcription factor?

 Off note, I have never tried any of those GO packages, so any advise/suggestion are welcome. Thank you so much in advance,

 D.

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