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What is the best tool for analyzing and visualazing gene ontologies at the moment? Any good suggestion?
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I personally think that WEGO (http://wego.genomics.org.cn/) is kinda widely used at the moment. I did also use CateGOrizer and quite satisfy with that (http://www.animalgenome.org/tools/catego/). Others including DAVID is also really good in analyzing GO http://david.abcc.ncifcrf.gov/ -
The same question, more detail:
I have the gene ontology annotation file in obo format and gene association file in gaf2 format. I want to visualize them with the purpose:
1. how many and what genes were assigned to one GO term?
2. How many and what GO terms assigned to one specific gene? And the relation between these terms.
3. Multiple GO terms or Genes searching, output the resulted GO DAG graphComment
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