There are many softwares available on-line now but each of them having some disadvantages. I wonder what's the best option. Thank you.
Yes, Affymetrix on Arabidopsis, not a rocket science, I am just curious if there is any easier way than AmiGO, that don't take more than 500, or Virtualplant that crushes quite often. .. I can use ATG as imput.
If you already have affymetrix IDS for the transcripts. Means, you already have annotations, then you can use the ids in the DAVID system https://david.ncifcrf.gov. It is a good web tool highly cited.
I suggest using the PANTHER database (http://pantherdb.org/). It can take a long gene list and has many options to customise including choice of organism and type of analysis. You can also look at the relevant Nature Protocols paper (2013) for further info (http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.092.html).
You may want to take a look at GOanna and other utilities at http://www.agbase.msstate.edu/.
Another useful tool BINGO (http://www.psb.ugent.be/cbd/papers/BiNGO/Tutorial.html) is available as a Cytoscape plugin, and performs few extended analyses as well.
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