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Gene Ontology


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#1 marek82313

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Posted 23 July 2009 - 07:35 AM

Hello everybody,

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,

Marco

#2 HomeBrew

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Posted 23 July 2009 - 09:09 AM

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".

#3 noelmathur

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Posted 23 July 2009 - 09:43 PM

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.

Edited by noelmathur, 23 July 2009 - 09:44 PM.


#4 marek82313

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Posted 23 July 2009 - 11:34 PM

Hello,

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?




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