You can use DEGseq package of R for purpose of annotating DE genes . There are numerous files available which can guide you.

Thanks Pankaj,and I wanted to classify the DE genes based on their molecular function, how can I achieve that?

I personally prefer using EdgeR to perform DE gene analysis. With regards to performing GO enrichment analysis on the DE gene list you obtained from the first step, you can either give goseq (http://bioconductor.org/packages/release/bioc/html/goseq.html) a try, or use publicly available GO enrichment analysis tools such as PantherDB (http://www.pantherdb.org). 

Hi Terry, thank you so much, I tried GOSeq but Arabidopsis is not supported in goseq package, is there any way to do GO enrichment analysis for unsupported organisms in goseq?

Thanks.

Actually, my bad. I didn't see the part that you've used cufflinks. In this case it doesn't make sense to use edgeR or DEGseq actually. Can't you use Panther DB to perform GO term enrichments for you? Arabidopsis proteins are well represented in the uni-rot database that Panther DB uses.

Hi Terry, I used panther db its good, what about DAVID? since it got a very recent update i am planning to give it a try.

Thanks for your help Terry.