Comparative Genomics Using Gene Ontology

Question

[Juan Ugalde]

Hi,

I searched for a similar question and couldn't find anything, so here it goes!. I'm interested in comparing multiple microbial genomes based on their gene ontology annotation. The goal is to look for categories that could be unique to certain genomes, as well as the core shared by multiple (if not all) genomes. Anyone has any ideas on tools and/or approaches to do this?. Most of the tools that I've found are focused on microarray/transcriptomic analysis.

Thanks for the advice!

Answer 1

[Qdjm]

Hi Juan, I think that the more standard way to do this is using Clusters of Orthologous Groups or COGs.

Note that if there isn't a curator annotating gene products for an organism, then there's no non-electronic (non-IEA) annotations for the organism. Here's a list of organisms with non-IEA annotations, as you can see, not many microbial genomes. And most IEA annotations are assigned by GOA using rules based on protein domains. So, if you still want to try using the Gene Ontology annotations, you could always set this up yourself.

You also might want to have a look at PANTHER

[Juan Ugalde]

Thanks for the comment!. I have a preliminary annotation of gene ontology categories based on the mapping of pfam categories. I forgot about Panther, but I will take a look.Thanks!

Answer 2

[SES]

Hi Juan, you normally see these analyses in the context of expression data because people are interested in the functional changes associated with a response to some stimulus (compare a background set of GO categories from a non-treated sample to those after a stress treatment and see what changed).

Have a look at this list on this site. There are quite a few discussions there that I have found helpful.