If you have a list of genes that are deferentially expressed, you can run enrichment analysis (not just DESeq results). I use ontologizer, which is a command line tool and very easy to run. Here is how to run:
Before you begin, you need to have 2 important files. 1. GO ontology file, where you describe every possible GO term numbers with what they are. You can easily get this from here: http://purl.obolibrary.org/obo/go.obo 2. Mapping file, this will describe the association of genes of the organism with GO terms (also available on GO website, if it is a well known organism, else you may have to generate your own).
Once you have these 2 files, you can run Ontologizer
Here the population.txt is basically the full list of genes that you have in anno file. The only time you need to change this is when you have a different background set to test. You can also play around the other settings like --mode, --resamplingsteps to optimize. With the -d it will also generate a dot file, that can be used with GraphViz to show the pathway where these genes are enriched.
To generate graphs:
dot -Tpng input.dot -o output.png
Hope this helps!
(you can also run BiNGO, a cytoscape plugin which is easier if you are new to command line!)