Analyzing microarray data: a tool for annotations and grouping genes? - (Jun/12/2008 )
I'm analyzing microarray data from yeast. We used to have geneSpring that can group genes (we find interesting) based on GO terms or function or some other specification. Is there a freely available tool that can do that?
R and the bioconductor - not a band, but a great language and set of tools for microarray analysis.
Many free tools can do GO analysis such as this one http://burgundy.cmmt.ubc.ca/GOToolBox/
You can find more by googling with "gene ontology analysis".
To use these programs, you need to get a list of genes from your microarray data such as a list of genes downregulated by certain treatment and use the list as input, these programs will tell you what GO terms are over- or under-represented in the list. Different programs may need different gene identifiers, such as gene symbol, unigene id, refseq id, etc.