Hello, everyone, sorry if my quesition is a bit silly, I am new to bioinformtics and Bioconductor. Why does GOstats resp. the GO annotation package use entrez gene ids? I thought, that GO terms are associated with proteins. And cause one gene can be translated to diffenent proteins, analyzation only with gene ids will perhaps be problematic. Especially if the data consists of miRNAs or Proteins and you have to convert it back to gene ids. So why does Bioconductor not use the annotation data from the Gene Ontology website. For example in the human annotation file, there are Uniprot and IPI identifiers annotated. Best regards, Kai

Kai Schlamp wrote: > Hello, everyone, > > sorry if my quesition is a bit silly, I am new to bioinformtics and > Bioconductor. Welcome - as with all list-servs there is a substantial body of past discussion and some etiquette. Please read the posting guide, and from that you will find that there are searchable mail archives, a good place to start from - eg searching on GO and EntrezID will give you a number of threads to look at. In general, when you have a question, spending a few minutes searching the discussion list will often turn up the answer. > Why does GOstats resp. the GO annotation package use entrez gene ids? > I thought, that GO terms are associated with proteins. And cause one > gene can be translated to diffenent proteins, analyzation only with gene > ids will perhaps be problematic. Do you have a reference for that? AFAIK that is not true and all mapping is via Entrez (or equivalent), but if you have some documentation that proves otherwise, we would all be happy to see it. > Especially if the data consists of miRNAs or Proteins and you have to > convert it back to gene ids. > So why does Bioconductor not use the annotation data from the Gene > Ontology website. For example in the human annotation file, there are > Uniprot and IPI identifiers annotated. Because that is not how it works. AFAIK we are not yet at the point where anyone can reliable distinguish different protein products in a high throughput assay (which is what the annotation packages are designed for). And in particular, if one is mapping from transcripts (eg microarrays - it is unlikely that there is sufficient resolution to know which potential mRNA is there - and even if so that would only cover those proteins with SNPs (or similar) in the region probed and would not address any post-translational modifications etc. Robert best wishes Robert > > Best regards, > Kai > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org