Gene Ontology - Looking for a good software (Jul/23/2009 )
I have to analyze a list of genes verifying if there's Gene Ontology Term enrichment and compare the frequency of each term to the one in the human genome (possibly obtaining a chart or a table).
Does anybody know any good and reliable software to do this?
Thanks in advance,
Have you tried the NIAID's DAVID suite?
Their description starts "For any given gene list, DAVID tools are able to:" and the first item on the list that follows is "Identify enriched biological themes, particularly GO terms".
Recently, I asked this question on microarray mailing list as well. I know Onto-Express can do it too. It didn't work for me due to some Java issues on my machine but the author, Sorin Draghici replied on the list that if I have any issues, I could contact him or his students directly for help.
This is a good option too, in case, if you don't understand how to analyze results further. I am more looking for a pie chart and author of Onto-Express claims that its possible with their program.
many thank to HomeBrew and noelmathur for the help, the David suite seems to be suitable to accomplish the tasks that I have, even seems to have some troubles recognizing and categorizing some genes of my list. I have not still tried using Onto-Express, if I understand correctly it seems to me to be a microarray-analysis oriented software, the fact is I don't have microarray data, but just a list of gene I've obtained through various in silico analysis.
Until now I used the Generic Gene Ontology Term Mapper to generate the ontologies and calculate the frequency of association of my genes with them, but it is unable to recognize some genes...
Does anybody know any other tools that I could use?