Gene symbols (if a reference annotation dataset was used with Cuffdiff) can be cut out of the output and used with a few different tools. Alternatively, the gene regions in the output can be intersected with a dataset of gene symbols with genome coordinates (UCSC is a good source for this type of data) - although be careful about this - a small overlap in gene bounds does not necessary mean that the two are a "match" - and if that was available to start with (for your specific reference genome) it is best used with Cuffdiff directly.
There are also methods of exploring cross-species gene matches (then inheriting annotation attached to those). The gotcha here is that reciprocal best match and/or overlap in a MAF/Conservation track and/or remapping to another reference genome through liftOver are not confirmation of Ortholog status. Confirmed Orthologs are the most trustworthy source of cross-species annotation.
There are three primary tools to explore first - search the tool panel by the keyword "ontology". The tool group "Phenotype Association" has other annotation options. Annovar (hg19) and SnpEff (ce10) could be another annotation choice if your reference genome is a match for the content indexed.
All of the above is based on the tool set on the Main Galaxy server - for others (to use in a local or cloud), search in the Tool Shed. Just be aware that keyword "GO", alone, is too short to use for searches. But, one can review other potential tools through google/publications, then see if a wrapper exists (or create a wrapper, if you have programming resource).
Hope this helps! Jen, Galaxy team
i want to compare the ontologies of genes generated from cuffdiff output and use it for BLAST2GO. Tried several options but for BLAST2GO , a fasta seq is required so i used gffread and then extract genomic DNA for fasta sequence . i have used the merged transcript file generated from cuffmerge . I dont know whether i am following the right track:
1. my aim is to compare the ontologies of differentially expressed genes in 2 samples
2. is there any way to know that which transcripts came from which sample because when i am using the merged transcript file it will give me the fasta seq but will it tell me which seq / transcript from which sample so that i can compare their ontologies in terms of gene expression.